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/7808390/working'
mkdir: created directory `/scratch/stefan/7808390/working/protonate'
Storing results in /scratch/stefan/7808390/finished
Working in /scratch/stefan/7808390/working
/scratch/stefan/7808390/working /scratch/stefan/7808390

/scratch/stefan/7808390/working/protonate /scratch/stefan/7808390/working /scratch/stefan/7808390
Precomputing protomers for all compounds (pH: 7.4)
ph 7.4: 1069 protomers created
Coalesing and merging protomers
1032 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1050 protomers after new stereo-center expansion
/scratch/stefan/7808390/working /scratch/stefan/7808390

Bulk generating 3D conformations all protomers in /scratch/stefan/7808390/working/3D
mkdir: created directory `/scratch/stefan/7808390/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7808390/working/protonate/xaaabka-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'
1051 3D conformations generated for 1000 compounds

Building REAL300025277150
mkdir: created directory `/scratch/stefan/7808390/working/building'
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277150'
/scratch/stefan/7808390/working/building/REAL300025277150 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277150

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277150/0 /scratch/stefan/7808390/working/building/REAL300025277150 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1
`/scratch/stefan/7808390/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277150 none CC(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 185, 201, 201, 184, 185, 184, 184, 184, 184, 150, 184, 94, 94, 38, 94, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 184, 184, 184, 184, 184, 184, 184, 184, 184, 150, 150, 94, 38, 38, 1] 603
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])
total number of confs: 1406
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: REAL300025277150 none CC(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 3, 7, 18, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 50, 65, 184, 184, 184, 184, 184, 7, 7, 7, 7, 18, 18, 54, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 50, 50, 184] 603
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 497
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277150 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277150
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `/scratch/stefan/7808390/finished'
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277150/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277150
Building REAL300025277151
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277151'
/scratch/stefan/7808390/working/building/REAL300025277151 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277151

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277151/0 /scratch/stefan/7808390/working/building/REAL300025277151 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/2
`/scratch/stefan/7808390/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CON=C1)

`REAL300025277151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277151 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CON=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [106, 87, 60, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 109, 109, 196, 196, 196, 196, 106, 106, 106, 87, 87, 60, 28, 28, 1, 106, 106, 106, 106, 106, 106, 196, 196] 196
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 576
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277151 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CON=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 47, 57, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 2, 2, 2, 5, 5, 13, 47, 47, 106, 1, 1, 1, 1, 1, 1, 14, 14] 196
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41])
total number of confs: 294
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277151 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CON=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 28, 68, 68, 68, 143, 157, 196, 196, 196, 196, 196, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 14, 14, 14, 28, 28, 68, 143, 143, 196, 14, 14, 14, 14, 14, 14, 1, 1] 196
rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 640
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277151 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277151
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277151/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277151
Building REAL300025277152
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277152'
/scratch/stefan/7808390/working/building/REAL300025277152 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277152

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277152/0 /scratch/stefan/7808390/working/building/REAL300025277152 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/3
`/scratch/stefan/7808390/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC(N)=N1)

`REAL300025277152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277152 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 108, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 178, 178, 201, 201, 201, 201, 201, 148, 148, 148, 108, 108, 64, 30, 30, 1, 148, 148, 148, 148, 148, 148, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277152 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 43, 61, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 2, 2, 2, 5, 5, 12, 43, 43, 148, 1, 1, 1, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277152 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 48, 48, 48, 122, 140, 201, 201, 201, 201, 201, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 22, 22, 48, 122, 122, 201, 11, 11, 11, 11, 11, 11, 1, 2, 2] 201
rigid atoms, others: [41, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277152 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277152
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277152/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277152
Building REAL300025277153
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277153'
/scratch/stefan/7808390/working/building/REAL300025277153 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277153

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277153/0 /scratch/stefan/7808390/working/building/REAL300025277153 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/4
`/scratch/stefan/7808390/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCO)

`REAL300025277153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277153 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [97, 66, 42, 42, 26, 42, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 181, 197, 201, 201, 97, 97, 97, 66, 66, 42, 26, 26, 1, 97, 97, 97, 97, 97, 97, 181, 181, 201, 201, 201, 201, 201, 201, 603] 603
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 1541
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: REAL300025277153 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 4, 7, 7, 7, 19, 25, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 2, 2, 7, 9, 10, 21, 2, 2, 2, 4, 4, 7, 19, 19, 97, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 21, 21, 63] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 343
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277153 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277153
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277153/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277153
Building REAL300025277154
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277154'
/scratch/stefan/7808390/working/building/REAL300025277154 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277154

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277154/0 /scratch/stefan/7808390/working/building/REAL300025277154 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/5
`/scratch/stefan/7808390/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(=O)C1CC1)

`REAL300025277154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277154 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [11, 11, 9, 9, 8, 9, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 12, 12, 13, 13, 11, 11, 11, 11, 11, 9, 8, 8, 1, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13] 13
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277154 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 3, 6, 6, 6, 9, 9, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 2, 2, 2, 3, 3, 6, 9, 9, 11, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 13
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277154 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [10, 10, 10, 11, 11, 11, 11, 12, 12, 13, 13, 13, 13, 13, 10, 10, 10, 10, 7, 10, 1, 7, 1, 1, 1, 10, 10, 10, 11, 11, 11, 12, 12, 13, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1] 13
rigid atoms, others: [40, 41, 42, 43, 44, 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])
total number of confs: 39
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277154 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277154
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277154/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277154
Building REAL300025277155
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277155'
/scratch/stefan/7808390/working/building/REAL300025277155 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277155

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277155/0 /scratch/stefan/7808390/working/building/REAL300025277155 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/6
`/scratch/stefan/7808390/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1COC(=O)N1)

`REAL300025277155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277155 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1COC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [61, 54, 41, 41, 21, 41, 11, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 62, 62, 74, 74, 74, 74, 74, 74, 61, 61, 61, 54, 54, 41, 21, 21, 1, 61, 61, 61, 61, 61, 61, 74, 74, 74] 74
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277155 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1COC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 42, 45, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 2, 2, 2, 3, 3, 11, 42, 42, 61, 1, 1, 1, 1, 1, 1, 7, 7, 7] 74
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277155 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1COC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 12, 29, 29, 29, 59, 62, 74, 74, 74, 74, 74, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 29, 59, 59, 74, 7, 7, 7, 7, 7, 7, 1, 1, 1] 74
rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 248
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277155 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277155
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277155/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277155
Building REAL300025277156
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277156'
/scratch/stefan/7808390/working/building/REAL300025277156 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277156

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277156/0 /scratch/stefan/7808390/working/building/REAL300025277156 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/7
`/scratch/stefan/7808390/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC(O)=C1)

`REAL300025277156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277156 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [144, 103, 61, 61, 30, 61, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 154, 154, 201, 201, 201, 201, 201, 201, 144, 144, 144, 103, 103, 61, 30, 30, 1, 144, 144, 144, 144, 144, 144, 201, 201, 402, 201] 402
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 1090
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: REAL300025277156 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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, 5, 13, 13, 13, 44, 58, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 2, 2, 2, 5, 5, 13, 44, 44, 144, 1, 1, 1, 1, 1, 1, 10, 10, 20, 10] 402
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 354
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: REAL300025277156 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 24, 43, 43, 43, 108, 132, 201, 201, 201, 201, 201, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 43, 108, 108, 201, 10, 10, 10, 10, 10, 10, 1, 1, 2, 1] 402
rigid atoms, others: [42, 43, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 613
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277156 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277156
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277156/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277156
Building REAL300025277157
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277157'
/scratch/stefan/7808390/working/building/REAL300025277157 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277157

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277157/0 /scratch/stefan/7808390/working/building/REAL300025277157 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/8
`/scratch/stefan/7808390/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CC1)

`REAL300025277157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277157 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [113, 93, 57, 57, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 115, 115, 186, 201, 201, 201, 113, 113, 113, 93, 93, 57, 27, 27, 1, 113, 113, 113, 113, 113, 113, 186, 186, 603, 201, 201, 201, 201] 603
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1462
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: REAL300025277157 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 5, 11, 11, 11, 41, 44, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 3, 3, 10, 27, 27, 27, 2, 2, 2, 5, 5, 11, 41, 41, 113, 1, 1, 1, 1, 1, 1, 10, 10, 81, 27, 27, 27, 27] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 420
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: REAL300025277157 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [27, 27, 27, 41, 84, 84, 84, 154, 157, 201, 201, 201, 201, 201, 27, 27, 27, 25, 8, 25, 1, 1, 1, 1, 1, 27, 27, 27, 41, 41, 84, 154, 154, 201, 27, 27, 27, 27, 27, 27, 8, 8, 6, 1, 1, 1, 1] 603
rigid atoms, others: [43, 44, 45, 46, 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, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 702
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277157 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277157
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277157/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277157
Building REAL300025277158
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277158'
/scratch/stefan/7808390/working/building/REAL300025277158 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277158

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277158/0 /scratch/stefan/7808390/working/building/REAL300025277158 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/9
`/scratch/stefan/7808390/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC1F)

`REAL300025277158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277158 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [162, 131, 86, 86, 35, 86, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 163, 163, 201, 201, 201, 201, 162, 162, 162, 131, 131, 86, 35, 35, 1, 162, 162, 162, 162, 162, 162, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277158 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 16, 16, 16, 59, 75, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 2, 2, 2, 5, 5, 16, 59, 59, 162, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45])
total number of confs: 405
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: REAL300025277158 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 53, 53, 53, 131, 150, 201, 201, 201, 201, 201, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 53, 131, 131, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 636
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277158 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277158
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277158/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277158
Building REAL300025277159
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277159'
/scratch/stefan/7808390/working/building/REAL300025277159 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277159

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277159/0 /scratch/stefan/7808390/working/building/REAL300025277159 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/10
`/scratch/stefan/7808390/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCCC#N)

`REAL300025277159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277159 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCCC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 59, 44, 44, 27, 44, 12, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 155, 178, 179, 178, 201, 201, 83, 83, 83, 59, 59, 44, 27, 27, 1, 83, 83, 83, 83, 83, 83, 155, 155, 179, 179, 179, 179, 179, 179, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277159 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCCC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 20, 26, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 2, 2, 8, 10, 12, 10, 20, 20, 2, 2, 2, 3, 3, 6, 20, 20, 83, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 20, 20] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277159 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277159
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277159/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277159
Building REAL300025277160
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277160'
/scratch/stefan/7808390/working/building/REAL300025277160 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277160

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277160/0 /scratch/stefan/7808390/working/building/REAL300025277160 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/11
`/scratch/stefan/7808390/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)SN=C1)

`REAL300025277160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277160 none CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)SN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'N.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 60, 71, 124, 124, 124, 124, 124, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 17, 60, 60, 124, 8] 154
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 338
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277160 none CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)SN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'N.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 20, 45, 45, 45, 106, 121, 154, 154, 154, 154, 154, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 45, 106, 106, 154, 1] 154
rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 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])
total number of confs: 517
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: REAL300025277160 none CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)SN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'N.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, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [154, 154, 127, 124, 127, 124, 124, 124, 124, 110, 124, 74, 74, 30, 74, 12, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 124, 124, 124, 124, 124, 124, 124, 124, 124, 110, 110, 74, 30, 30, 1, 154] 154
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])
total number of confs: 540
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277160 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277160
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277160/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277160
Building REAL300025277161
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277161'
/scratch/stefan/7808390/working/building/REAL300025277161 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277161

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277161/0 /scratch/stefan/7808390/working/building/REAL300025277161 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/12
`/scratch/stefan/7808390/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)C1CCC1)

`REAL300025277161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277161 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 97, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 135, 135, 159, 159, 201, 201, 201, 134, 134, 134, 97, 97, 48, 29, 29, 1, 134, 134, 134, 134, 134, 134, 159, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 858
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277161 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 30, 37, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 2, 2, 7, 7, 14, 14, 14, 2, 2, 2, 5, 5, 10, 30, 30, 134, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277161 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 54, 54, 54, 122, 133, 201, 201, 201, 201, 201, 14, 14, 14, 13, 5, 13, 1, 5, 1, 1, 1, 1, 14, 14, 14, 28, 28, 54, 122, 122, 201, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 20, 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, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277161 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277161
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277161/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277161
Building REAL300025277162
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277162'
/scratch/stefan/7808390/working/building/REAL300025277162 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277162

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277162/0 /scratch/stefan/7808390/working/building/REAL300025277162 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/13
`/scratch/stefan/7808390/working/3D/13' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC(F)F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277162 none CC(OC(F)F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [44, 41, 44, 46, 49, 49, 41, 41, 41, 41, 41, 41, 31, 41, 20, 20, 13, 20, 10, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 49, 41, 41, 41, 41, 41, 41, 41, 41, 41, 31, 31, 20, 13, 13, 1] 49
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])
total number of confs: 189
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: REAL300025277162 none CC(OC(F)F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [6, 2, 6, 10, 14, 14, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 24, 24, 39, 39, 39, 39, 39, 6, 6, 6, 6, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 24, 24, 39] 48
rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 167
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277162 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277162
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277162/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277162
Building REAL300025277163
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277163'
/scratch/stefan/7808390/working/building/REAL300025277163 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277163

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277163/0 /scratch/stefan/7808390/working/building/REAL300025277163 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/14
`/scratch/stefan/7808390/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1)

`REAL300025277163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277163 none CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 53, 78, 164, 164, 164, 164, 164, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 21, 53, 53, 164] 201
rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277163 none CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 11, 11, 22, 47, 47, 47, 100, 129, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 47, 100, 100, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 5] 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277163 none CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 183, 164, 183, 164, 164, 164, 164, 126, 164, 73, 73, 31, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 164, 164, 164, 164, 126, 126, 73, 31, 31, 1] 201
rigid atoms, others: [49, 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])
total number of confs: 771
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277163 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277163
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277163/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277163
Building REAL300025277164
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277164'
/scratch/stefan/7808390/working/building/REAL300025277164 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277164

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277164/0 /scratch/stefan/7808390/working/building/REAL300025277164 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/15
`/scratch/stefan/7808390/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1)

`REAL300025277164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277164 none C#CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 39, 55, 146, 146, 146, 146, 146, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 13, 39, 39, 146] 201
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 327
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277164 none C#CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 10, 10, 10, 10, 10, 10, 24, 48, 48, 48, 124, 142, 201, 201, 201, 201, 201, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 48, 124, 124, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 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: REAL300025277164 none C#CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 171, 146, 171, 146, 146, 146, 146, 111, 146, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 146, 146, 146, 146, 146, 146, 146, 146, 146, 111, 111, 62, 30, 30, 1] 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])
total number of confs: 732
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277164 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277164
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277164/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277164
Building REAL300025277165
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277165'
/scratch/stefan/7808390/working/building/REAL300025277165 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277165

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277165/0 /scratch/stefan/7808390/working/building/REAL300025277165 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/16
`/scratch/stefan/7808390/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNC=N1)

`REAL300025277165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277165 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [163, 124, 75, 75, 32, 75, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 171, 171, 201, 201, 201, 201, 201, 201, 163, 163, 163, 124, 124, 75, 32, 32, 1, 163, 163, 163, 163, 163, 163, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 785
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277165 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 5, 11, 11, 11, 39, 66, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 4, 4, 11, 11, 15, 15, 15, 15, 2, 2, 2, 5, 5, 11, 39, 39, 163, 1, 1, 1, 1, 1, 1, 11, 11, 15, 15, 15] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277165 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [15, 15, 15, 30, 50, 50, 50, 112, 140, 201, 201, 201, 201, 201, 15, 15, 15, 12, 4, 11, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 50, 112, 112, 201, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277165 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277165
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277165/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277165
Building REAL300025277166
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277166'
/scratch/stefan/7808390/working/building/REAL300025277166 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277166

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277166/0 /scratch/stefan/7808390/working/building/REAL300025277166 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/17
`/scratch/stefan/7808390/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1)

`REAL300025277166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277166 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [161, 121, 77, 77, 32, 77, 13, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 161, 161, 161, 121, 121, 77, 32, 32, 1, 161, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 791
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277166 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 4, 8, 8, 8, 32, 56, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 3, 3, 10, 10, 23, 23, 23, 23, 2, 2, 2, 4, 4, 8, 32, 32, 161, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277166 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 35, 57, 57, 57, 124, 147, 201, 201, 201, 201, 201, 17, 17, 17, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 35, 35, 57, 124, 124, 201, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277166 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277166
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277166/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277166
Building REAL300025277167
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277167'
/scratch/stefan/7808390/working/building/REAL300025277167 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277167

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277167/0 /scratch/stefan/7808390/working/building/REAL300025277167 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/18
`/scratch/stefan/7808390/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1)

`REAL300025277167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277167 none CCC1(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [11, 11, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 40, 59, 151, 151, 151, 151, 151, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 40, 40, 151, 11, 11, 11, 11] 201
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 351
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: REAL300025277167 none CCC1(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [3, 1, 1, 1, 4, 9, 9, 11, 11, 11, 11, 11, 11, 21, 43, 43, 43, 101, 124, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 43, 101, 101, 201, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 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, 48])
total number of confs: 609
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: REAL300025277167 none CCC1(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [201, 201, 190, 154, 151, 154, 151, 151, 151, 151, 116, 151, 62, 62, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 151, 151, 151, 151, 151, 151, 151, 151, 151, 116, 116, 62, 31, 31, 1, 201, 201, 201, 201] 201
rigid atoms, others: [48, 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, 49, 50, 51, 52])
total number of confs: 879
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277167 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277167
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277167/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277167
Building REAL300025277168
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277168'
/scratch/stefan/7808390/working/building/REAL300025277168 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277168

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277168/0 /scratch/stefan/7808390/working/building/REAL300025277168 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/19
`/scratch/stefan/7808390/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNN=C1)

`REAL300025277168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277168 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [148, 102, 60, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 150, 150, 201, 201, 201, 201, 201, 201, 148, 148, 148, 102, 102, 60, 29, 29, 1, 148, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 788
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277168 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 5, 9, 9, 9, 34, 51, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 3, 3, 10, 10, 22, 22, 22, 22, 2, 2, 2, 5, 5, 9, 34, 34, 148, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
total number of confs: 335
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277168 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CNN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 29, 49, 49, 49, 121, 150, 201, 201, 201, 201, 201, 19, 19, 19, 18, 6, 18, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 29, 29, 49, 121, 121, 201, 19, 19, 19, 19, 19, 19, 6, 6, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/7808390/working/building/REAL300025277168 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277168
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277168/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277168
Building REAL300025277169
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277169'
/scratch/stefan/7808390/working/building/REAL300025277169 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277169

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277169/0 /scratch/stefan/7808390/working/building/REAL300025277169 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/20
`/scratch/stefan/7808390/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1CF)

`REAL300025277169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277169 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [119, 96, 56, 56, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 121, 121, 201, 201, 201, 201, 201, 201, 119, 119, 119, 96, 96, 56, 26, 26, 1, 119, 119, 119, 119, 119, 119, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 748
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277169 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 11, 11, 11, 43, 45, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 39, 2, 2, 2, 5, 5, 11, 43, 43, 118, 1, 1, 1, 1, 1, 1, 10, 10, 39, 39] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
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: REAL300025277169 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 47, 47, 47, 123, 125, 201, 201, 201, 201, 201, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 20, 20, 47, 123, 123, 201, 10, 10, 10, 10, 10, 10, 1, 1, 8, 8] 201
rigid atoms, others: [42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45])
total number of confs: 620
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277169 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277169
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277169/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277169
Building REAL300025277170
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277170'
/scratch/stefan/7808390/working/building/REAL300025277170 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277170

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277170/0 /scratch/stefan/7808390/working/building/REAL300025277170 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/21
`/scratch/stefan/7808390/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=NS1)

`REAL300025277170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277170 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 60, 43, 43, 22, 43, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 142, 201, 201, 201, 201, 77, 77, 77, 60, 60, 43, 22, 22, 1, 77, 77, 77, 77, 77, 77, 142, 142, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277170 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 32, 34, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 2, 2, 2, 3, 3, 8, 32, 32, 77, 1, 1, 1, 1, 1, 1, 7, 7, 16] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([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, 41, 42, 43])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277170 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 31, 62, 62, 62, 157, 159, 201, 201, 201, 201, 201, 17, 16, 16, 16, 4, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 62, 157, 157, 201, 17, 17, 17, 16, 16, 16, 4, 4, 1] 201
rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 722
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277170 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277170
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277170/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277170
Building REAL300025277171
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277171'
/scratch/stefan/7808390/working/building/REAL300025277171 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277171

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277171/0 /scratch/stefan/7808390/working/building/REAL300025277171 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/22
`/scratch/stefan/7808390/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=C1CCC1)

`REAL300025277171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277171 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 114, 59, 59, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 160, 160, 201, 201, 201, 201, 201, 155, 155, 155, 114, 114, 59, 28, 28, 1, 155, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 792
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277171 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 40, 55, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 2, 2, 2, 5, 5, 12, 40, 40, 155, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277171 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 46, 46, 112, 133, 201, 201, 201, 201, 201, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 24, 46, 112, 112, 201, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277171 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277171
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277171/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277171
Building REAL300025277172
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277172'
/scratch/stefan/7808390/working/building/REAL300025277172 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277172

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277172/0 /scratch/stefan/7808390/working/building/REAL300025277172 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/23
`/scratch/stefan/7808390/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277172 none CCC(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
564  conformations in input
total number of sets (complete confs): 564
using faster count positions algorithm for large data
unique positions, atoms: [175, 169, 112, 169, 188, 112, 112, 112, 112, 112, 112, 94, 112, 58, 58, 26, 58, 13, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 169, 188, 188, 564, 112, 112, 112, 112, 112, 112, 112, 112, 112, 94, 94, 58, 26, 26, 1] 564
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])
total number of confs: 1611
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277172 none CCC(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
564  conformations in input
total number of sets (complete confs): 564
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 2, 5, 21, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 38, 40, 112, 112, 112, 112, 112, 8, 8, 8, 8, 8, 5, 21, 21, 63, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 38, 38, 112] 564
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 413
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277172 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277172
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277172/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277172
Building REAL300025277173
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277173'
/scratch/stefan/7808390/working/building/REAL300025277173 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277173

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277173/0 /scratch/stefan/7808390/working/building/REAL300025277173 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/24
`/scratch/stefan/7808390/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277173 none CC(C)(O)C(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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: [31, 29, 31, 31, 25, 29, 25, 25, 25, 25, 25, 25, 24, 25, 19, 19, 13, 19, 9, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 93, 29, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 19, 13, 13, 1] 93
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])
total number of confs: 218
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: REAL300025277173 none CC(C)(O)C(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 4, 6, 6, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 19, 19, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 18, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 19, 19, 25] 93
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 131
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277173 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277173
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277173/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277173
Building REAL300025277174
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277174'
/scratch/stefan/7808390/working/building/REAL300025277174 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277174

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277174/0 /scratch/stefan/7808390/working/building/REAL300025277174 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/25
`/scratch/stefan/7808390/working/3D/25' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(O)C1CC1)

`REAL300025277174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277174 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [121, 87, 46, 46, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 125, 125, 173, 178, 178, 201, 201, 121, 121, 121, 87, 87, 46, 27, 27, 1, 121, 121, 121, 121, 121, 121, 173, 173, 178, 534, 201, 201, 201, 201, 201] 603
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 1429
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277174 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 4, 8, 8, 8, 26, 37, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 2, 2, 6, 11, 11, 22, 22, 2, 2, 2, 4, 4, 8, 26, 26, 121, 1, 1, 1, 1, 1, 1, 6, 6, 11, 33, 22, 22, 22, 22, 22] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277174 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [22, 22, 22, 36, 62, 62, 62, 118, 138, 201, 201, 201, 201, 201, 22, 22, 22, 21, 10, 21, 4, 1, 4, 1, 1, 1, 22, 22, 22, 36, 36, 62, 118, 118, 201, 22, 22, 22, 22, 22, 22, 10, 10, 4, 12, 1, 1, 1, 1, 1] 603
rigid atoms, others: [45, 46, 47, 48, 49, 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, 42, 43, 44])
total number of confs: 684
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277174 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277174
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277174/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277174
Building REAL300025277175
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277175'
/scratch/stefan/7808390/working/building/REAL300025277175 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277175

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277175/0 /scratch/stefan/7808390/working/building/REAL300025277175 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/26
`/scratch/stefan/7808390/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277175 none CC(C)CC(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 171, 201, 164, 171, 164, 164, 164, 164, 127, 164, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 164, 164, 164, 164, 127, 127, 64, 29, 29, 1] 201
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])
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: REAL300025277175 none CC(C)CC(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 9, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 39, 60, 164, 164, 164, 164, 164, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 13, 39, 39, 164] 201
rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277175 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277175
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277175/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277175
Building REAL300025277176
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277176'
/scratch/stefan/7808390/working/building/REAL300025277176 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277176

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277176/0 /scratch/stefan/7808390/working/building/REAL300025277176 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/27
`/scratch/stefan/7808390/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C#CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1)

`REAL300025277176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277176 none CC1(C#CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 43, 50, 71, 71, 71, 71, 71, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 43, 43, 71, 3, 3, 3, 3] 71
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 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])
total number of confs: 217
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277176 none CC1(C#CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 16, 16, 16, 44, 51, 71, 71, 71, 71, 71, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 16, 44, 44, 71, 1, 1, 1, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 46, 47, 48, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 209
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277176 none CC1(C#CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 62, 71, 48, 48, 27, 48, 12, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 62, 62, 48, 27, 27, 1, 71, 71, 71, 71] 71
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: 264
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277176 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277176
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277176/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277176
Building REAL300025277177
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277177'
/scratch/stefan/7808390/working/building/REAL300025277177 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277177

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277177/0 /scratch/stefan/7808390/working/building/REAL300025277177 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/28
`/scratch/stefan/7808390/working/3D/28' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC1CC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277177 none CC(=CC1CC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 19, 19, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 27, 37, 128, 128, 128, 128, 128, 8, 8, 8, 8, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 27, 27, 128] 201
rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 295
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277177 none CC(=CC1CC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 5, 17, 17, 19, 19, 19, 19, 19, 19, 31, 55, 55, 55, 119, 138, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 31, 31, 55, 119, 119, 201] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 34, 30, 31] set([0, 1, 6, 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, 46, 47, 48, 49])
total number of confs: 650
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: REAL300025277177 none CC(=CC1CC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 131, 201, 201, 201, 201, 128, 131, 128, 128, 128, 128, 79, 128, 46, 46, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 128, 128, 128, 128, 79, 79, 46, 26, 26, 1] 201
rigid atoms, others: [49, 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])
total number of confs: 795
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277177 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277177
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277177/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277177
Building REAL300025277178
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277178'
/scratch/stefan/7808390/working/building/REAL300025277178 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277178

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277178/0 /scratch/stefan/7808390/working/building/REAL300025277178 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/29
`/scratch/stefan/7808390/working/3D/29' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@@H]1C#N)

`REAL300025277178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277178 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [35, 34, 30, 30, 23, 30, 11, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 36, 36, 37, 37, 37, 37, 37, 37, 35, 35, 35, 34, 34, 30, 23, 23, 1, 35, 35, 35, 35, 35, 35, 37, 37] 37
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277178 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 8, 8, 8, 19, 22, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 2, 2, 2, 4, 4, 8, 19, 19, 35, 1, 1, 1, 1, 1, 1, 6, 6] 37
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
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: REAL300025277178 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 8, 13, 13, 13, 23, 24, 37, 37, 37, 37, 37, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 13, 23, 23, 37, 6, 6, 6, 6, 6, 6, 1, 1] 37
rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 111
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277178 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277178
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277178/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277178
Building REAL300025277179
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277179'
/scratch/stefan/7808390/working/building/REAL300025277179 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277179

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277179/0 /scratch/stefan/7808390/working/building/REAL300025277179 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/30
`/scratch/stefan/7808390/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=COC=N1)

`REAL300025277179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277179 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=COC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [167, 125, 66, 66, 29, 66, 12, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 175, 175, 201, 201, 201, 201, 201, 201, 167, 167, 167, 125, 125, 66, 29, 29, 1, 167, 167, 167, 167, 167, 167, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 789
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277179 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=COC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 13, 13, 13, 41, 66, 167, 167, 167, 167, 167, 1, 1, 1, 1, 1, 4, 4, 10, 10, 16, 16, 16, 16, 2, 2, 2, 6, 6, 13, 41, 41, 167, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277179 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=COC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 56, 56, 56, 124, 141, 201, 201, 201, 201, 201, 16, 16, 16, 13, 4, 12, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 33, 33, 56, 124, 124, 201, 16, 16, 16, 16, 16, 16, 4, 4, 1, 1] 201
rigid atoms, others: [44, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/7808390/working/building/REAL300025277179 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277179
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277179/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277179
Building REAL300025277180
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277180'
/scratch/stefan/7808390/working/building/REAL300025277180 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277180

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277180/0 /scratch/stefan/7808390/working/building/REAL300025277180 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/31
`/scratch/stefan/7808390/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CCC1)

`REAL300025277180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277180 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [130, 106, 65, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 186, 201, 201, 201, 201, 201, 130, 130, 130, 106, 106, 65, 30, 30, 1, 130, 130, 130, 130, 130, 130, 186, 186, 201, 201, 603, 201, 201, 201, 201, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1461
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277180 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 4, 8, 8, 8, 31, 48, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 2, 2, 6, 14, 19, 14, 14, 14, 2, 2, 2, 4, 4, 8, 31, 31, 130, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 57, 14, 14, 14, 14, 14, 14] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 386
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277180 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [14, 14, 14, 24, 42, 42, 42, 100, 127, 201, 201, 201, 201, 201, 14, 14, 14, 14, 6, 14, 1, 1, 1, 6, 1, 1, 1, 14, 14, 14, 24, 24, 42, 100, 100, 201, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 18, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [47, 48, 49, 50, 51, 20, 21, 22, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 639
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277180 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277180
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277180/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277180
Building REAL300025277181
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277181'
/scratch/stefan/7808390/working/building/REAL300025277181 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277181

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277181/0 /scratch/stefan/7808390/working/building/REAL300025277181 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/32
`/scratch/stefan/7808390/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CO1)

`REAL300025277181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277181 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [99, 71, 44, 44, 25, 44, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 109, 109, 188, 201, 201, 201, 201, 99, 99, 99, 71, 71, 44, 25, 25, 1, 99, 99, 99, 99, 99, 99, 188, 188, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 805
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277181 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 4, 9, 9, 9, 26, 34, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 3, 3, 11, 19, 19, 19, 19, 2, 2, 2, 4, 4, 9, 26, 26, 99, 1, 1, 1, 1, 1, 1, 11, 11, 19, 19] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 258
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277181 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [19, 19, 19, 33, 49, 49, 49, 100, 107, 201, 201, 201, 201, 201, 19, 19, 19, 17, 5, 17, 1, 1, 1, 1, 1, 1, 19, 19, 19, 33, 33, 49, 100, 100, 201, 19, 19, 19, 19, 19, 19, 5, 5, 1, 1] 201
rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/7808390/working/building/REAL300025277181 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277181
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277181/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277181
Building REAL300025277182
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277182'
/scratch/stefan/7808390/working/building/REAL300025277182 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277182

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277182/0 /scratch/stefan/7808390/working/building/REAL300025277182 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/33
`/scratch/stefan/7808390/working/3D/33' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CC=CCC1)

`REAL300025277182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277182 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 39, 39, 25, 39, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 176, 201, 201, 201, 201, 201, 201, 94, 94, 94, 64, 64, 39, 25, 25, 1, 94, 94, 94, 94, 94, 94, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277182 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 20, 28, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 8, 20, 20, 20, 20, 20, 20, 2, 2, 2, 4, 4, 8, 20, 20, 94, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277182 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 61, 61, 61, 109, 121, 201, 201, 201, 201, 201, 20, 20, 20, 20, 6, 20, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 36, 36, 61, 109, 109, 201, 20, 20, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/7808390/working/building/REAL300025277182 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277182
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277182/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277182
Building REAL300025277183
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277183'
/scratch/stefan/7808390/working/building/REAL300025277183 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277183

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277183/0 /scratch/stefan/7808390/working/building/REAL300025277183 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/34
`/scratch/stefan/7808390/working/3D/34' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CC2CC2C1)

`REAL300025277183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277183 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 12, 12, 11, 12, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 15, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 12, 11, 11, 1, 14, 14, 14, 14, 14, 14, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16] 16
rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277183 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 2, 3, 3, 3, 7, 9, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 3, 7, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5] 16
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277183 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 6, 6, 6, 9, 11, 16, 16, 16, 16, 16, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 9, 9, 16, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 16
rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 49
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277183 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277183
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277183/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277183
Building REAL300025277184
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277184'
/scratch/stefan/7808390/working/building/REAL300025277184 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277184

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277184/0 /scratch/stefan/7808390/working/building/REAL300025277184 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/35
`/scratch/stefan/7808390/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2CC2C1)

`REAL300025277184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277184 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 34, 34, 24, 34, 12, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 185, 201, 201, 201, 201, 201, 85, 85, 85, 57, 57, 34, 24, 24, 1, 85, 85, 85, 85, 85, 85, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 856
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277184 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 20, 27, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 2, 2, 2, 4, 4, 8, 20, 20, 85, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277184 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 60, 60, 60, 112, 124, 201, 201, 201, 201, 201, 19, 19, 19, 19, 5, 19, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 37, 37, 60, 112, 112, 201, 19, 19, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/7808390/working/building/REAL300025277184 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277184
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277184/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277184
Building REAL300025277185
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277185'
/scratch/stefan/7808390/working/building/REAL300025277185 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277185

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277185/0 /scratch/stefan/7808390/working/building/REAL300025277185 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/36
`/scratch/stefan/7808390/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CF)=C1)

`REAL300025277185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277185 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CF)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 103, 59, 59, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 173, 173, 201, 201, 201, 201, 201, 201, 143, 143, 143, 103, 103, 59, 28, 28, 1, 143, 143, 143, 143, 143, 143, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 732
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277185 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CF)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 35, 52, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 21, 7, 2, 2, 2, 5, 5, 9, 35, 35, 143, 1, 1, 1, 1, 1, 1, 21, 21, 7] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
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: REAL300025277185 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CF)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 14, 26, 26, 26, 86, 111, 201, 201, 201, 201, 201, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 7, 1, 7, 7, 7, 14, 14, 26, 86, 86, 201, 7, 7, 7, 7, 7, 7, 7, 7, 1] 201
rigid atoms, others: [44, 18, 20, 21, 22, 23, 24, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 562
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277185 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277185
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277185/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277185
Building REAL300025277186
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277186'
/scratch/stefan/7808390/working/building/REAL300025277186 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277186

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277186/0 /scratch/stefan/7808390/working/building/REAL300025277186 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/37
`/scratch/stefan/7808390/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCC1)

`REAL300025277186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277186 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [99, 85, 63, 63, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 100, 100, 119, 119, 119, 119, 99, 99, 99, 85, 85, 63, 31, 31, 1, 99, 99, 99, 99, 99, 99, 119, 119, 119, 119, 119] 119
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 415
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: REAL300025277186 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 42, 53, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 2, 2, 2, 5, 5, 13, 42, 42, 99, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 119
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44])
total number of confs: 266
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: REAL300025277186 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 17, 37, 37, 37, 79, 90, 119, 119, 119, 119, 119, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 37, 79, 79, 119, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 119
rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 389
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277186 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277186
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277186/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277186
Building REAL300025277187
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277187'
/scratch/stefan/7808390/working/building/REAL300025277187 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277187

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277187/0 /scratch/stefan/7808390/working/building/REAL300025277187 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/38
`/scratch/stefan/7808390/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277187 none CC(C)(O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 173, 201, 201, 173, 125, 125, 125, 125, 125, 125, 125, 85, 125, 47, 47, 27, 47, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 173, 173, 173, 173, 125, 125, 125, 125, 125, 125, 125, 125, 125, 85, 85, 47, 27, 27, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1540
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277187 none CC(C)(O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 8, 20, 20, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 26, 35, 125, 125, 125, 125, 125, 20, 20, 20, 20, 20, 20, 60, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 26, 26, 125] 603
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277187 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277187
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277187/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277187
Building REAL300025277188
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277188'
/scratch/stefan/7808390/working/building/REAL300025277188 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277188

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277188/0 /scratch/stefan/7808390/working/building/REAL300025277188 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/39
`/scratch/stefan/7808390/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277188 none CC(C)(C)C(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 67, 75, 75, 67, 67, 67, 67, 67, 67, 61, 67, 43, 43, 24, 43, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 225, 67, 67, 67, 67, 67, 67, 67, 67, 67, 61, 61, 43, 24, 24, 1] 225
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 534
number of broken/clashed sets: 184
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277188 none CC(C)(C)C(CO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 4, 2, 3, 8, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 28, 29, 67, 67, 67, 67, 67, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 24, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 28, 28, 67] 225
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 224
number of broken/clashed sets: 184
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277188 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277188
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277188/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277188
Building REAL300025277189
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277189'
/scratch/stefan/7808390/working/building/REAL300025277189 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277189

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277189/0 /scratch/stefan/7808390/working/building/REAL300025277189 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/40
`/scratch/stefan/7808390/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N1)

`REAL300025277189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277189 none CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 33, 46, 139, 139, 139, 139, 139, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 33, 33, 139, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 292
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277189 none CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 11, 11, 11, 11, 11, 11, 23, 45, 45, 45, 103, 123, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 45, 103, 103, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 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: 600
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: REAL300025277189 none CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 163, 139, 163, 139, 139, 139, 139, 97, 139, 52, 52, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 139, 139, 139, 139, 97, 97, 52, 29, 29, 1, 201] 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])
total number of confs: 741
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277189 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277189
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277189/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277189
Building REAL300025277190
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277190'
/scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277190

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277190/0 /scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/41
`/scratch/stefan/7808390/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277190 none C[N@@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 58, 75, 127, 127, 127, 127, 127, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 16, 58, 58, 127] 143
rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 44, 16, 40, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277190 none C[N@@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 16, 33, 33, 33, 80, 95, 143, 143, 143, 143, 143, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 33, 80, 80, 143] 143
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: 422
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277190 none C[N@@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 143, 143, 143, 143, 129, 127, 129, 127, 127, 127, 127, 114, 127, 66, 66, 30, 66, 12, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 127, 127, 127, 127, 127, 127, 127, 127, 127, 114, 114, 66, 30, 30, 1] 143
rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 562
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277190/1 /scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/42
`/scratch/stefan/7808390/working/3D/42' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277190.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277190/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277190 none C[N@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 19, 23, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 19, 19, 43] 43
rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 44, 16, 40, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277190 none C[N@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 24, 28, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 18, 24, 24, 43] 43
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: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277190 none C[N@H+]1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 41, 43, 30, 30, 21, 30, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 41, 41, 30, 21, 21, 1] 43
rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 163
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277190/2 /scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/43
`/scratch/stefan/7808390/working/3D/43' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277190.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277190/2/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: REAL300025277190 none CN1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 59, 85, 171, 171, 171, 171, 171, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 17, 59, 59, 171] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 7, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277190 none CN1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 7, 7, 7, 7, 7, 7, 17, 36, 36, 36, 101, 131, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 36, 101, 101, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 36, 38, 5, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277190 none CN1CCCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 171, 196, 171, 171, 171, 171, 136, 171, 76, 76, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 171, 171, 171, 171, 171, 136, 136, 76, 31, 31, 1] 201
rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 786
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277190 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277190
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277190/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277190/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277190/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277190
Building REAL300025277191
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277191'
/scratch/stefan/7808390/working/building/REAL300025277191 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277191

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277191/0 /scratch/stefan/7808390/working/building/REAL300025277191 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/44
`/scratch/stefan/7808390/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCC1)

`REAL300025277191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277191 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [85, 69, 52, 52, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 87, 87, 87, 87, 87, 85, 85, 85, 69, 69, 52, 28, 28, 1, 85, 85, 85, 85, 85, 85, 87, 87, 87, 87, 87] 87
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025277191 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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, 5, 12, 12, 12, 42, 52, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 2, 2, 2, 5, 5, 12, 42, 42, 85, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 87
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277191 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [9, 9, 9, 19, 31, 31, 31, 61, 69, 87, 87, 87, 87, 87, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 10, 10, 10, 19, 19, 31, 61, 61, 87, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1] 87
rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 284
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277191 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277191
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277191/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277191
Building REAL300025277192
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277192'
/scratch/stefan/7808390/working/building/REAL300025277192 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277192

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277192/0 /scratch/stefan/7808390/working/building/REAL300025277192 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/45
`/scratch/stefan/7808390/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1)

`REAL300025277192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277192 none CC1CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [12, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 51, 78, 163, 163, 163, 163, 163, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 51, 51, 163] 201
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 387
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277192 none CC1CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 29, 58, 58, 58, 124, 147, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 58, 124, 124, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29, 30, 31] set([5, 6, 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, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277192 none CC1CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [201, 201, 201, 167, 163, 167, 163, 163, 163, 163, 126, 163, 63, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 163, 163, 163, 163, 163, 163, 126, 126, 63, 29, 29, 1] 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])
total number of confs: 716
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277192 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277192
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277192/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277192
Building REAL300025277193
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277193'
/scratch/stefan/7808390/working/building/REAL300025277193 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277193

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277193/0 /scratch/stefan/7808390/working/building/REAL300025277193 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/46
`/scratch/stefan/7808390/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCCC[C@H]1O)

`REAL300025277193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277193 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCCC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [171, 142, 92, 92, 32, 92, 12, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 188, 188, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 142, 142, 92, 32, 32, 1, 171, 171, 171, 171, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 603] 603
rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1374
number of broken/clashed sets: 106
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277193 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCCC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 4, 10, 10, 10, 41, 73, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 10, 41, 41, 171, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 21] 603
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 386
number of broken/clashed sets: 106
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277193 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCCC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 13, 29, 29, 29, 97, 139, 201, 201, 201, 201, 201, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 29, 97, 97, 201, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3] 603
rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 52])
total number of confs: 551
number of broken/clashed sets: 106
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277193 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277193
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277193/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277193
Building REAL300025277194
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277194'
/scratch/stefan/7808390/working/building/REAL300025277194 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277194

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277194/0 /scratch/stefan/7808390/working/building/REAL300025277194 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/47
`/scratch/stefan/7808390/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2(CC2)C1)

`REAL300025277194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277194 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2(CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 37, 37, 26, 37, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 183, 201, 201, 201, 201, 201, 96, 96, 96, 61, 61, 37, 26, 26, 1, 96, 96, 96, 96, 96, 96, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277194 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2(CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 7, 18, 25, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 2, 2, 2, 3, 3, 7, 18, 18, 96, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277194 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC2(CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 61, 61, 61, 119, 130, 201, 201, 201, 201, 201, 21, 21, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 37, 37, 61, 119, 119, 201, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 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.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277194 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277194
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277194/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277194
Building REAL300025277195
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277195'
/scratch/stefan/7808390/working/building/REAL300025277195 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277195

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277195/0 /scratch/stefan/7808390/working/building/REAL300025277195 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/48
`/scratch/stefan/7808390/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1C)

`REAL300025277195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277195 none CC1=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 30, 41, 109, 109, 109, 109, 109, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 30, 30, 109, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 246
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277195 none CC1=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 25, 53, 53, 53, 111, 132, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 53, 111, 111, 201, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 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, 45, 47, 48, 49])
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: REAL300025277195 none CC1=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 121, 109, 121, 109, 109, 109, 109, 81, 109, 49, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 109, 109, 109, 109, 109, 81, 81, 49, 30, 30, 1, 201, 201, 201, 201] 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: 615
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277195 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277195
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277195/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277195
Building REAL300025277196
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277196'
/scratch/stefan/7808390/working/building/REAL300025277196 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277196

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277196/0 /scratch/stefan/7808390/working/building/REAL300025277196 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/49
`/scratch/stefan/7808390/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)OCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277196 none CN1C(=O)OCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 6, 7, 7, 7, 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, 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: [6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 39, 42, 63, 63, 63, 63, 63, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 11, 39, 39, 63] 71
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 196
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277196 none CN1C(=O)OCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 6, 7, 7, 7, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 9, 27, 27, 27, 55, 59, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 27, 55, 55, 71] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 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, 46, 47])
total number of confs: 246
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: REAL300025277196 none CN1C(=O)OCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 64, 63, 64, 63, 63, 63, 63, 51, 63, 40, 40, 23, 40, 12, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 63, 63, 63, 63, 63, 63, 63, 63, 63, 51, 51, 40, 23, 23, 1] 71
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 266
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277196 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277196
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277196/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277196
Building REAL300025277197
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277197'
/scratch/stefan/7808390/working/building/REAL300025277197 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277197

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277197/0 /scratch/stefan/7808390/working/building/REAL300025277197 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/50
`/scratch/stefan/7808390/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277197 none CC(CF)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [200, 175, 200, 201, 174, 175, 174, 174, 174, 174, 141, 174, 81, 81, 35, 81, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 201, 201, 174, 174, 174, 174, 174, 174, 174, 174, 174, 141, 141, 81, 35, 35, 1] 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])
total number of confs: 840
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277197 none CC(CF)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 49, 59, 174, 174, 174, 174, 174, 7, 7, 7, 7, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 49, 49, 174] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 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])
total number of confs: 449
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277197 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277197
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277197/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277197
Building REAL300025277198
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277198'
/scratch/stefan/7808390/working/building/REAL300025277198 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277198

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277198/0 /scratch/stefan/7808390/working/building/REAL300025277198 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/51
`/scratch/stefan/7808390/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(Cl)=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277198 none CC(Cl)=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 79, 79, 79, 79, 79, 79, 79, 69, 79, 53, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 79, 79, 79, 79, 79, 79, 79, 79, 79, 69, 69, 53, 30, 30, 1] 90
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])
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: REAL300025277198 none CC(Cl)=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 40, 46, 79, 79, 79, 79, 79, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 40, 40, 79] 90
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277198 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277198
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277198/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277198
Building REAL300025277199
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277199'
/scratch/stefan/7808390/working/building/REAL300025277199 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277199

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277199/0 /scratch/stefan/7808390/working/building/REAL300025277199 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/52
`/scratch/stefan/7808390/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277199 none CC=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 103, 103, 103, 103, 103, 103, 103, 93, 103, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 103, 103, 103, 103, 103, 103, 103, 103, 103, 93, 93, 64, 30, 30, 1] 108
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])
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: REAL300025277199 none CC=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 52, 62, 103, 103, 103, 103, 103, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 13, 52, 52, 103] 108
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277199 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277199
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277199/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277199
Building REAL300025277200
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277200'
/scratch/stefan/7808390/working/building/REAL300025277200 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277200

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277200/0 /scratch/stefan/7808390/working/building/REAL300025277200 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/53
`/scratch/stefan/7808390/working/3D/53' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)NCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277200 none CN1C(=O)NCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 38, 43, 61, 61, 61, 61, 61, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 13, 38, 38, 61] 61
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39, 38] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277200 none CN1C(=O)NCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 44, 49, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 18, 44, 44, 61] 61
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: 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: REAL300025277200 none CN1C(=O)NCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 54, 61, 40, 40, 23, 40, 12, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 54, 54, 40, 23, 23, 1] 61
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 228
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277200 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277200
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277200/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277200
Building REAL300025277201
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277201'
/scratch/stefan/7808390/working/building/REAL300025277201 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277201

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277201/0 /scratch/stefan/7808390/working/building/REAL300025277201 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/54
`/scratch/stefan/7808390/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1F)

`REAL300025277201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277201 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 110, 59, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 161, 161, 201, 201, 201, 201, 201, 201, 144, 144, 144, 110, 110, 59, 30, 30, 1, 144, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 810
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277201 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 46, 64, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 2, 2, 2, 5, 5, 15, 46, 46, 144, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277201 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 43, 43, 43, 107, 130, 201, 201, 201, 201, 201, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 43, 107, 107, 201, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 51, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 584
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277201 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277201
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277201/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277201
Building REAL300025277202
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277202'
/scratch/stefan/7808390/working/building/REAL300025277202 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277202

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277202/0 /scratch/stefan/7808390/working/building/REAL300025277202 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/55
`/scratch/stefan/7808390/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCC(=O)O1)

`REAL300025277202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277202 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [84, 74, 49, 49, 26, 49, 11, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 86, 86, 94, 94, 94, 94, 94, 94, 84, 84, 84, 74, 74, 49, 26, 26, 1, 84, 84, 84, 84, 84, 84, 94, 94, 94, 94] 94
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 370
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277202 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 41, 46, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 2, 2, 2, 3, 3, 11, 41, 41, 84, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 94
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277202 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CCC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 12, 28, 28, 28, 69, 73, 94, 94, 94, 94, 94, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 28, 69, 69, 94, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 94
rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 299
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277202 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277202
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277202/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277202
Building REAL300025277203
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277203'
/scratch/stefan/7808390/working/building/REAL300025277203 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277203

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277203/0 /scratch/stefan/7808390/working/building/REAL300025277203 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/56
`/scratch/stefan/7808390/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1COC[C@H]1O)

`REAL300025277203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277203 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1COC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [135, 98, 53, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 138, 138, 195, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 98, 98, 53, 30, 30, 1, 135, 135, 135, 135, 135, 135, 195, 195, 201, 201, 201, 201, 603] 603
rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 1485
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: REAL300025277203 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1COC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 10, 10, 10, 29, 45, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 2, 2, 10, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 5, 5, 10, 29, 29, 135, 1, 1, 1, 1, 1, 1, 10, 10, 20, 20, 20, 20, 60] 603
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 393
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: REAL300025277203 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1COC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 34, 55, 55, 55, 110, 125, 201, 201, 201, 201, 201, 20, 20, 20, 18, 5, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 34, 34, 55, 110, 110, 201, 20, 20, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 3] 603
rigid atoms, others: [46, 47, 48, 49, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50])
total number of confs: 622
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277203 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277203
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277203/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277203
Building REAL300025277204
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277204'
/scratch/stefan/7808390/working/building/REAL300025277204 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277204

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277204/0 /scratch/stefan/7808390/working/building/REAL300025277204 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/57
`/scratch/stefan/7808390/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2CCOCC21)

`REAL300025277204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277204 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2CCOCC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [174, 154, 90, 90, 30, 90, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 174, 174, 176, 176, 176, 176, 176, 176, 174, 174, 174, 154, 154, 90, 30, 30, 1, 174, 174, 174, 174, 174, 174, 176, 176, 176, 176, 176, 176, 176, 176, 176] 176
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 652
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277204 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2CCOCC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 8, 22, 22, 22, 74, 106, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 22, 74, 74, 174, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 176
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 451
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277204 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2CCOCC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 11, 25, 25, 25, 80, 112, 176, 176, 176, 176, 176, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 25, 80, 80, 176, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 176
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 457
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277204 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277204
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277204/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277204
Building REAL300025277205
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277205'
/scratch/stefan/7808390/working/building/REAL300025277205 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277205

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277205/0 /scratch/stefan/7808390/working/building/REAL300025277205 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/58
`/scratch/stefan/7808390/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CCF)

`REAL300025277205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277205 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [136, 117, 73, 73, 32, 73, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 137, 137, 200, 200, 200, 136, 136, 136, 117, 117, 73, 32, 32, 1, 136, 136, 136, 136, 136, 136, 200, 200, 200, 200] 200
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277205 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 40, 47, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 3, 3, 11, 11, 49, 2, 2, 2, 5, 5, 12, 40, 40, 134, 1, 1, 1, 1, 1, 1, 11, 11, 49, 49] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42])
total number of confs: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277205 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277205
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277205/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277205
Building REAL300025277206
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277206'
/scratch/stefan/7808390/working/building/REAL300025277206 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277206

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277206/0 /scratch/stefan/7808390/working/building/REAL300025277206 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/59
`/scratch/stefan/7808390/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CC1)

`REAL300025277206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277206 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [119, 86, 42, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 158, 158, 170, 201, 201, 119, 119, 119, 86, 86, 42, 28, 28, 1, 119, 119, 119, 119, 119, 119, 158, 170, 170, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277206 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 31, 37, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 2, 2, 4, 4, 9, 14, 14, 2, 2, 2, 5, 5, 10, 31, 31, 119, 1, 1, 1, 1, 1, 1, 4, 9, 9, 14, 14, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277206 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 47, 47, 47, 106, 114, 201, 201, 201, 201, 201, 14, 14, 14, 14, 8, 14, 3, 8, 1, 1, 1, 1, 14, 14, 14, 26, 26, 47, 106, 106, 201, 14, 14, 14, 14, 14, 14, 8, 3, 3, 1, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 48, 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, 41, 42, 43])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277206 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277206
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277206/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277206
Building REAL300025277207
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277207'
/scratch/stefan/7808390/working/building/REAL300025277207 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277207

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277207/0 /scratch/stefan/7808390/working/building/REAL300025277207 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/60
`/scratch/stefan/7808390/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1)

`REAL300025277207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277207 none CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 70, 70, 70, 70, 70, 70, 70, 46, 70, 32, 32, 24, 32, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 70, 70, 70, 70, 70, 70, 70, 70, 70, 46, 46, 32, 24, 24, 1, 201, 201, 201, 201, 201] 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, 54])
total number of confs: 872
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277207 none CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 13, 18, 70, 70, 70, 70, 70, 15, 17, 17, 21, 21, 21, 21, 21, 15, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 13, 13, 70, 17, 17, 17, 17, 17] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 39, 12, 11, 40, 35, 36, 38, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 239
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: REAL300025277207 none CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 1, 3, 8, 17, 17, 17, 17, 17, 17, 17, 17, 29, 47, 47, 47, 87, 104, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 6, 6, 6, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 29, 29, 47, 87, 87, 201, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 50, 51, 52, 53, 54, 24, 25, 26] set([0, 1, 3, 4, 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, 48, 49])
total number of confs: 611
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277207 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277207
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277207/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277207
Building REAL300025277208
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277208'
/scratch/stefan/7808390/working/building/REAL300025277208 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277208

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277208/0 /scratch/stefan/7808390/working/building/REAL300025277208 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/61
`/scratch/stefan/7808390/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277208 none CC(C)CCC(=O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 131, 99, 131, 99, 99, 99, 99, 99, 99, 80, 99, 61, 61, 28, 61, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 99, 99, 99, 99, 99, 99, 99, 99, 99, 80, 80, 61, 28, 28, 1] 201
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277208 none CC(C)CCC(=O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 21, 40, 99, 99, 99, 99, 99, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 21, 21, 99] 201
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277208 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277208
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277208/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277208
Building REAL300025277209
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277209'
/scratch/stefan/7808390/working/building/REAL300025277209 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277209

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277209/0 /scratch/stefan/7808390/working/building/REAL300025277209 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/62
`/scratch/stefan/7808390/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277209 none C[N@@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 9, 11, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 9, 9, 15, 3, 3] 15
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277209 none C[N@@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 9, 11, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 15, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 52, 33, 27, 51, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277209 none C[N@@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 13, 14, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 13, 1, 15, 15] 15
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52])
total number of confs: 46
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277209 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277209/1 /scratch/stefan/7808390/working/building/REAL300025277209 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/63
`/scratch/stefan/7808390/working/3D/63' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277209.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277209/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277209 none C[N@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 10, 12, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 10, 10, 15, 3, 3] 15
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277209 none C[N@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 10, 12, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 15, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 52, 33, 27, 51, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277209 none C[N@H+]1CCC(=CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 13, 14, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 13, 1, 15, 15] 15
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52])
total number of confs: 44
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277209 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277209
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277209/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277209/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277209
Building REAL300025277210
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277210'
/scratch/stefan/7808390/working/building/REAL300025277210 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277210

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277210/0 /scratch/stefan/7808390/working/building/REAL300025277210 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/64
`/scratch/stefan/7808390/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277210 none CC1=C(C)NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 54, 74, 168, 168, 168, 168, 168, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 20, 54, 54, 168] 201
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277210 none CC1=C(C)NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 9, 9, 9, 9, 9, 9, 24, 48, 48, 48, 116, 146, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 48, 116, 116, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 26] set([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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277210 none CC1=C(C)NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 168, 189, 168, 168, 168, 168, 125, 168, 67, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 168, 168, 168, 168, 125, 125, 67, 30, 30, 1] 201
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])
total number of confs: 761
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277210 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277210
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277210/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277210
Building REAL300025277211
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277211'
/scratch/stefan/7808390/working/building/REAL300025277211 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277211

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277211/0 /scratch/stefan/7808390/working/building/REAL300025277211 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/65
`/scratch/stefan/7808390/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1COC(=O)N1)

`REAL300025277211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277211 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1COC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [58, 53, 38, 38, 20, 38, 10, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 59, 59, 69, 69, 69, 69, 69, 69, 58, 58, 58, 53, 53, 38, 20, 20, 1, 58, 58, 58, 58, 58, 58, 69, 69, 69] 69
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277211 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1COC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 38, 41, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 2, 3, 3, 11, 38, 38, 58, 1, 1, 1, 1, 1, 1, 7, 7, 7] 69
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
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: REAL300025277211 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1COC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 12, 26, 26, 26, 54, 58, 69, 69, 69, 69, 69, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 26, 54, 54, 69, 7, 7, 7, 7, 7, 7, 1, 1, 1] 69
rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 233
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277211 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277211
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277211/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277211
Building REAL300025277212
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277212'
/scratch/stefan/7808390/working/building/REAL300025277212 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277212

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277212/0 /scratch/stefan/7808390/working/building/REAL300025277212 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/66
`/scratch/stefan/7808390/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCC#N)

`REAL300025277212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277212 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 63, 42, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 148, 163, 164, 201, 201, 91, 91, 91, 63, 63, 42, 28, 28, 1, 91, 91, 91, 91, 91, 91, 148, 148, 164, 164, 164, 164, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 933
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277212 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 24, 28, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 2, 2, 8, 10, 11, 21, 21, 2, 2, 2, 4, 4, 8, 24, 24, 91, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 286
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277212 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277212
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277212/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277212
Building REAL300025277213
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277213'
/scratch/stefan/7808390/working/building/REAL300025277213 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277213

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277213/0 /scratch/stefan/7808390/working/building/REAL300025277213 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/67
`/scratch/stefan/7808390/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NO1)

`REAL300025277213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277213 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [182, 149, 95, 95, 34, 95, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 186, 186, 192, 192, 192, 192, 182, 182, 182, 149, 149, 95, 34, 34, 1, 182, 182, 182, 182, 182, 182, 192, 192] 192
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 711
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277213 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 21, 21, 21, 81, 108, 182, 182, 182, 182, 182, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 2, 2, 2, 6, 6, 21, 81, 81, 182, 1, 1, 1, 1, 1, 1, 11, 11] 192
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41])
total number of confs: 480
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277213 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 11, 11, 23, 62, 62, 62, 136, 160, 192, 192, 192, 192, 192, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 11, 11, 11, 23, 23, 62, 136, 136, 192, 11, 11, 11, 11, 11, 11, 1, 1] 192
rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 620
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277213 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277213
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277213/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277213
Building REAL300025277214
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277214'
/scratch/stefan/7808390/working/building/REAL300025277214 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277214

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277214/0 /scratch/stefan/7808390/working/building/REAL300025277214 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/68
`/scratch/stefan/7808390/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NC(=O)NN2)CCCN1C(=O)CN=[N+]=[N-])

`REAL300025277214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277214 none CC1(CNC(=O)CSC2=NC(=O)NN2)CCCN1C(=O)CN=[N+]=[N-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', '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, 14, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 4, 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: [80, 62, 39, 39, 26, 39, 11, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 149, 201, 201, 80, 80, 80, 62, 62, 39, 26, 26, 1, 1, 80, 80, 80, 80, 80, 80, 149, 149] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025277214 none CC1(CNC(=O)CSC2=NC(=O)NN2)CCCN1C(=O)CN=[N+]=[N-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', '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, 14, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 4, 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, 6, 12, 12, 12, 35, 60, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 2, 2, 10, 43, 43, 2, 2, 2, 6, 6, 12, 35, 35, 80, 80, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41])
total number of confs: 285
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277214 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277214/1 /scratch/stefan/7808390/working/building/REAL300025277214 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/69
`/scratch/stefan/7808390/working/3D/69' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NC(=O)[N-]N2)CCCN1C(=O)CN=[N+]=[N-])

`REAL300025277214.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277214/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277214 none CC1(CNC(=O)CSC2=NC(=O)[N-]N2)CCCN1C(=O)CN=[N+]=[N-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', '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, 14, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 4, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [59, 49, 31, 31, 17, 31, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 119, 169, 169, 59, 59, 59, 49, 49, 31, 17, 17, 1, 59, 59, 59, 59, 59, 59, 119, 119] 169
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 595
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277214 none CC1(CNC(=O)CSC2=NC(=O)[N-]N2)CCCN1C(=O)CN=[N+]=[N-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', '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, 14, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 4, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 9, 9, 9, 32, 33, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 3, 3, 11, 54, 54, 2, 2, 2, 3, 3, 9, 32, 32, 59, 1, 1, 1, 1, 1, 1, 11, 11] 169
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40])
total number of confs: 252
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277214 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277214
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277214/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277214/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277214
Building REAL300025277215
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277215'
/scratch/stefan/7808390/working/building/REAL300025277215 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277215

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277215/0 /scratch/stefan/7808390/working/building/REAL300025277215 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/70
`/scratch/stefan/7808390/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)N1)

`REAL300025277215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277215 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [75, 63, 47, 47, 24, 47, 12, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 76, 76, 88, 88, 88, 88, 88, 75, 75, 75, 63, 63, 47, 24, 24, 1, 75, 75, 75, 75, 75, 75, 88, 88, 88, 88, 88, 88] 88
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277215 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 40, 45, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 3, 3, 11, 40, 40, 75, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 88
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277215 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 9, 26, 26, 26, 63, 70, 88, 88, 88, 88, 88, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 26, 63, 63, 88, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 88
rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 278
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277215 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277215
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277215/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277215
Building REAL300025277216
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277216'
/scratch/stefan/7808390/working/building/REAL300025277216 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277216

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277216/0 /scratch/stefan/7808390/working/building/REAL300025277216 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/71
`/scratch/stefan/7808390/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCSC1)

`REAL300025277216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277216 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 114, 64, 64, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 162, 162, 201, 201, 201, 201, 201, 150, 150, 150, 114, 114, 64, 31, 31, 1, 150, 150, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 739
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277216 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 39, 59, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 2, 2, 2, 5, 5, 13, 39, 39, 150, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 327
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: REAL300025277216 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 37, 37, 99, 126, 201, 201, 201, 201, 201, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 37, 99, 99, 201, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 571
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277216 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277216
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277216/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277216
Building REAL300025277217
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277217'
/scratch/stefan/7808390/working/building/REAL300025277217 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277217

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277217/0 /scratch/stefan/7808390/working/building/REAL300025277217 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/72
`/scratch/stefan/7808390/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277217 none C[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens need rotated
267  conformations in input
total number of sets (complete confs): 267
using faster count positions algorithm for large data
unique positions, atoms: [89, 88, 89, 89, 88, 88, 88, 88, 88, 88, 79, 88, 60, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 267, 88, 88, 88, 88, 88, 88, 88, 88, 88, 79, 79, 60, 29, 29, 1] 267
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])
total number of confs: 597
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: REAL300025277217 none C[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens need rotated
267  conformations in input
total number of sets (complete confs): 267
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 5, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 46, 55, 88, 88, 88, 88, 88, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 46, 46, 88] 267
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 279
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277217 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277217
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277217/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277217
Building REAL300025277218
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277218'
/scratch/stefan/7808390/working/building/REAL300025277218 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277218

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277218/0 /scratch/stefan/7808390/working/building/REAL300025277218 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/73
`/scratch/stefan/7808390/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)O1)

`REAL300025277218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277218 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [186, 152, 97, 97, 34, 97, 13, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 198, 198, 201, 201, 201, 201, 201, 186, 186, 186, 152, 152, 97, 34, 34, 1, 186, 186, 186, 186, 186, 186, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025277218 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 6, 20, 20, 20, 76, 102, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 2, 2, 2, 6, 6, 20, 76, 76, 186, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 470
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277218 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [10, 10, 10, 23, 57, 57, 57, 137, 161, 201, 201, 201, 201, 201, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 57, 137, 137, 201, 10, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277218 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277218
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277218/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277218
Building REAL300025277219
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277219'
/scratch/stefan/7808390/working/building/REAL300025277219 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277219

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277219/0 /scratch/stefan/7808390/working/building/REAL300025277219 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/74
`/scratch/stefan/7808390/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277219 none CON=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 162, 155, 162, 155, 155, 155, 155, 119, 155, 70, 70, 32, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 155, 155, 155, 155, 155, 155, 155, 155, 155, 119, 119, 70, 32, 32, 1] 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])
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: REAL300025277219 none CON=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 39, 60, 155, 155, 155, 155, 155, 15, 15, 15, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 39, 39, 155] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 356
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277219 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277219
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277219/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277219
Building REAL300025277220
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277220'
/scratch/stefan/7808390/working/building/REAL300025277220 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277220

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277220/0 /scratch/stefan/7808390/working/building/REAL300025277220 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/75
`/scratch/stefan/7808390/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N=[N+]=[N-])

`REAL300025277220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277220 none CC(C)(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N=[N+]=[N-] 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [154, 141, 154, 111, 111, 111, 111, 111, 111, 111, 80, 111, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 154, 154, 154, 154, 154, 154, 141, 141, 111, 111, 111, 111, 111, 111, 111, 111, 111, 80, 80, 58, 30, 30, 1] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277220 none CC(C)(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N=[N+]=[N-] 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 26, 40, 111, 111, 111, 111, 111, 7, 15, 15, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 26, 26, 111] 201
rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 270
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277220 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277220
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277220/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277220
Building REAL300025277221
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277221'
/scratch/stefan/7808390/working/building/REAL300025277221 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277221

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277221/0 /scratch/stefan/7808390/working/building/REAL300025277221 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/76
`/scratch/stefan/7808390/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(F)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277221 none CC1(F)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 41, 58, 154, 154, 154, 154, 154, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 41, 41, 154, 10, 10] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277221 none CC1(F)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 10, 10, 10, 10, 10, 10, 22, 44, 44, 44, 115, 132, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 44, 115, 115, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 25, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277221 none CC1(F)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 154, 158, 154, 154, 154, 154, 110, 154, 59, 59, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 154, 154, 154, 154, 110, 110, 59, 28, 28, 1, 201, 201] 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])
total number of confs: 800
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277221 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277221
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277221/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277221
Building REAL300025277222
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277222'
/scratch/stefan/7808390/working/building/REAL300025277222 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277222

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277222/0 /scratch/stefan/7808390/working/building/REAL300025277222 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/77
`/scratch/stefan/7808390/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277222 none CC(C)[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [36, 34, 36, 27, 34, 34, 27, 27, 27, 27, 27, 27, 23, 27, 17, 17, 12, 17, 8, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 102, 27, 27, 27, 27, 27, 27, 27, 27, 27, 23, 23, 17, 12, 12, 1] 108
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])
total number of confs: 254
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277222 none CC(C)[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 9, 3, 6, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 17, 17, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 17, 17, 27] 108
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 135
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277222 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277222
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277222/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277222
Building REAL300025277223
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277223'
/scratch/stefan/7808390/working/building/REAL300025277223 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277223

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277223/0 /scratch/stefan/7808390/working/building/REAL300025277223 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/78
`/scratch/stefan/7808390/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277223 none CN(C)C(=O)C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 185, 201, 185, 144, 144, 144, 144, 144, 144, 144, 102, 144, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 185, 185, 144, 144, 144, 144, 144, 144, 144, 144, 144, 102, 102, 63, 30, 30, 1] 201
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 797
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277223 none CN(C)C(=O)C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 18, 6, 16, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 26, 42, 144, 144, 144, 144, 144, 18, 18, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 26, 26, 144] 201
rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 310
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277223 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277223
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277223/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277223
Building REAL300025277224
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277224'
/scratch/stefan/7808390/working/building/REAL300025277224 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277224

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277224/0 /scratch/stefan/7808390/working/building/REAL300025277224 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/79
`/scratch/stefan/7808390/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CCC(=O)O1)

`REAL300025277224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277224 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CCC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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: [124, 99, 68, 68, 33, 68, 12, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 125, 125, 147, 147, 147, 147, 147, 147, 124, 124, 124, 99, 99, 68, 33, 33, 1, 124, 124, 124, 124, 124, 124, 147, 147, 147, 147] 147
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 564
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277224 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CCC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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: [1, 1, 1, 5, 18, 18, 18, 63, 73, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 18, 63, 63, 124, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 147
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
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: REAL300025277224 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CCC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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, 9, 9, 20, 45, 45, 45, 108, 117, 147, 147, 147, 147, 147, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 45, 108, 108, 147, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 147
rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 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.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277224 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277224
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277224/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277224
Building REAL300025277225
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277225'
/scratch/stefan/7808390/working/building/REAL300025277225 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277225

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277225/0 /scratch/stefan/7808390/working/building/REAL300025277225 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/80
`/scratch/stefan/7808390/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(C)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277225 none CC1=CN(C)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 35, 48, 138, 138, 138, 138, 138, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 35, 35, 138] 201
rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 298
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277225 none CC1=CN(C)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 10, 10, 10, 10, 10, 10, 20, 43, 43, 43, 103, 124, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 43, 103, 103, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277225 none CC1=CN(C)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 138, 155, 138, 138, 138, 138, 105, 138, 54, 54, 28, 54, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 138, 138, 138, 105, 105, 54, 28, 28, 1] 201
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 712
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277225 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277225
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277225/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277225
Building REAL300025277226
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277226'
/scratch/stefan/7808390/working/building/REAL300025277226 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277226

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277226/0 /scratch/stefan/7808390/working/building/REAL300025277226 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/81
`/scratch/stefan/7808390/working/3D/81' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC=CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277226 none C=CC=CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 86, 86, 86, 86, 86, 86, 86, 59, 86, 37, 37, 25, 37, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 176, 86, 86, 86, 86, 86, 86, 86, 86, 86, 59, 59, 37, 25, 25, 1] 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])
total number of confs: 866
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277226 none C=CC=CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 16, 23, 86, 86, 86, 86, 86, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 16, 16, 86] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277226 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277226
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277226/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277226
Building REAL300025277227
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277227'
/scratch/stefan/7808390/working/building/REAL300025277227 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277227

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277227/0 /scratch/stefan/7808390/working/building/REAL300025277227 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/82
`/scratch/stefan/7808390/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277227 none C[N@@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 8, 8, 8] 8
rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277227 none C[N@@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 4, 4, 4, 4, 4, 4, 4, 4, 5, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 6, 8, 8, 8] 8
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277227 none C[N@@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 8, 7, 8, 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, 8, 7, 7, 7, 6, 6, 1] 8
rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 20
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277227 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277227/1 /scratch/stefan/7808390/working/building/REAL300025277227 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/83
`/scratch/stefan/7808390/working/3D/83' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277227.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277227/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277227 none C[N@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 17, 17, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 9, 17, 17, 19] 19
rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277227 none C[N@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 9, 17, 17, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 17, 17, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277227 none C[N@H+]1CCC[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 19, 14, 14, 10, 14, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 14, 10, 10, 1] 19
rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 65
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277227 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277227
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277227/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277227/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277227
Building REAL300025277228
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277228'
/scratch/stefan/7808390/working/building/REAL300025277228 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277228

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277228/0 /scratch/stefan/7808390/working/building/REAL300025277228 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/84
`/scratch/stefan/7808390/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC=CC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277228 none CCCC=CC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 187, 187, 162, 144, 162, 144, 144, 144, 144, 144, 144, 115, 144, 91, 91, 32, 91, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 187, 187, 162, 486, 144, 144, 144, 144, 144, 144, 144, 144, 144, 115, 115, 91, 32, 32, 1] 603
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 1313
number of broken/clashed sets: 175
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277228 none CCCC=CC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 13, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 23, 50, 144, 144, 144, 144, 144, 13, 13, 13, 13, 13, 13, 13, 5, 5, 3, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 23, 23, 144] 603
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 326
number of broken/clashed sets: 175
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277228 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277228
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277228/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277228
Building REAL300025277229
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277229'
/scratch/stefan/7808390/working/building/REAL300025277229 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277229

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277229/0 /scratch/stefan/7808390/working/building/REAL300025277229 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/85
`/scratch/stefan/7808390/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC=CCO1)

`REAL300025277229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277229 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC=CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [161, 126, 75, 75, 32, 75, 13, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 180, 180, 201, 201, 201, 201, 201, 161, 161, 161, 126, 126, 75, 32, 32, 1, 161, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 777
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277229 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC=CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
201  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, 20, 20, 20, 53, 78, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 2, 2, 2, 7, 7, 20, 53, 53, 161, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 396
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: REAL300025277229 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC=CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 46, 46, 46, 106, 131, 201, 201, 201, 201, 201, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 22, 22, 46, 106, 106, 201, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 567
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277229 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277229
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277229/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277229
Building REAL300025277230
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277230'
/scratch/stefan/7808390/working/building/REAL300025277230 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277230

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277230/0 /scratch/stefan/7808390/working/building/REAL300025277230 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/86
`/scratch/stefan/7808390/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CO1)

`REAL300025277230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277230 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 95, 57, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 169, 169, 201, 201, 201, 201, 130, 130, 130, 95, 95, 57, 29, 29, 1, 130, 130, 130, 130, 130, 130, 169, 169, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 729
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277230 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 31, 46, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 3, 3, 7, 7, 18, 18, 17, 18, 2, 2, 2, 5, 5, 9, 31, 31, 130, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277230 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 34, 60, 60, 60, 122, 143, 201, 201, 201, 201, 201, 18, 18, 18, 16, 6, 16, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 34, 34, 60, 122, 122, 201, 18, 18, 18, 18, 18, 18, 6, 6, 1, 1] 201
rigid atoms, others: [44, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 648
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277230 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277230
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277230/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277230
Building REAL300025277231
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277231'
/scratch/stefan/7808390/working/building/REAL300025277231 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277231

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277231/0 /scratch/stefan/7808390/working/building/REAL300025277231 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/87
`/scratch/stefan/7808390/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277231 none CC(CC1CCC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 19, 19, 19, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 20, 27, 95, 95, 95, 95, 95, 5, 5, 5, 5, 11, 11, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 20, 20, 95] 201
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277231 none CC(CC1CCC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 10, 18, 18, 19, 19, 19, 19, 19, 19, 34, 60, 60, 60, 109, 127, 201, 201, 201, 201, 201, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 34, 34, 60, 109, 109, 201] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 39, 34, 35, 36, 38, 37] set([0, 1, 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, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277231 none CC(CC1CCC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 96, 153, 168, 201, 201, 201, 95, 96, 95, 95, 95, 95, 63, 95, 39, 39, 26, 39, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 168, 168, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95, 95, 95, 95, 95, 95, 63, 63, 39, 26, 26, 1] 201
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 904
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277231 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277231
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277231/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277231
Building REAL300025277232
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277232'
/scratch/stefan/7808390/working/building/REAL300025277232 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277232

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277232/0 /scratch/stefan/7808390/working/building/REAL300025277232 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/88
`/scratch/stefan/7808390/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC2(C1)N=N2)

`REAL300025277232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277232 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC2(C1)N=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 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: [122, 101, 67, 67, 32, 67, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 122, 122, 144, 144, 144, 144, 144, 144, 122, 122, 122, 101, 101, 67, 32, 32, 1, 122, 122, 122, 122, 122, 122, 144, 144, 144, 144, 144, 144, 144] 144
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277232 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC2(C1)N=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 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, 5, 15, 15, 15, 57, 69, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 15, 57, 57, 122, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 144
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 337
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277232 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC2(C1)N=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 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, 6, 15, 38, 38, 38, 95, 111, 144, 144, 144, 144, 144, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 38, 95, 95, 144, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 144
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 452
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277232 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277232
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277232/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277232
Building REAL300025277233
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277233'
/scratch/stefan/7808390/working/building/REAL300025277233 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277233

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277233/0 /scratch/stefan/7808390/working/building/REAL300025277233 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/89
`/scratch/stefan/7808390/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277233 none CC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 38, 58, 137, 137, 137, 137, 137, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 38, 38, 137, 12, 12] 201
rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277233 none CC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 12, 12, 12, 12, 12, 12, 26, 50, 50, 50, 117, 134, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 50, 117, 117, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277233 none CC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 137, 175, 137, 137, 137, 137, 94, 137, 60, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 137, 137, 137, 137, 94, 94, 60, 30, 30, 1, 201, 201] 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])
total number of confs: 739
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277233 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277233
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277233/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277233
Building REAL300025277234
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277234'
/scratch/stefan/7808390/working/building/REAL300025277234 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277234

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277234/0 /scratch/stefan/7808390/working/building/REAL300025277234 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/90
`/scratch/stefan/7808390/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=NNC=C1)

`REAL300025277234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277234 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=NNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens 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, 92, 72, 72, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 123, 182, 184, 201, 201, 201, 201, 123, 123, 123, 92, 92, 72, 31, 31, 1, 123, 123, 123, 123, 123, 123, 182, 182, 184, 184, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 800
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: REAL300025277234 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=NNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 29, 47, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 7, 8, 19, 19, 19, 19, 2, 2, 2, 3, 3, 6, 29, 29, 123, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 19, 19, 19] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([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, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 290
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: REAL300025277234 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=NNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens 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, 29, 43, 43, 43, 98, 122, 201, 201, 201, 201, 201, 19, 19, 19, 19, 11, 19, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 29, 29, 43, 98, 98, 201, 19, 19, 19, 19, 19, 19, 11, 11, 6, 6, 1, 1, 1] 201
rigid atoms, others: [46, 47, 48, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 620
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277234 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277234
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277234/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277234
Building REAL300025277235
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277235'
/scratch/stefan/7808390/working/building/REAL300025277235 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277235

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277235/0 /scratch/stefan/7808390/working/building/REAL300025277235 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/91
`/scratch/stefan/7808390/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)OC[C@@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1)

`REAL300025277235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277235 none CC1(C)OC[C@@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 54, 75, 171, 171, 171, 171, 171, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 54, 54, 171] 201
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277235 none CC1(C)OC[C@@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 11, 23, 50, 50, 50, 114, 132, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 50, 114, 114, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277235 none CC1(C)OC[C@@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in 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, 201, 171, 182, 171, 171, 171, 171, 126, 171, 66, 66, 30, 66, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 171, 171, 171, 171, 171, 126, 126, 66, 30, 30, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 782
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277235 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277235
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277235/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277235
Building REAL300025277236
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277236'
/scratch/stefan/7808390/working/building/REAL300025277236 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277236

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277236/0 /scratch/stefan/7808390/working/building/REAL300025277236 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/92
`/scratch/stefan/7808390/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C#CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277236 none CN(C)C(=O)C#CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 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, 193, 193, 188, 193, 188, 188, 188, 188, 169, 188, 109, 109, 36, 109, 13, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 188, 188, 188, 188, 188, 188, 188, 188, 188, 169, 169, 109, 36, 36, 1] 193
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277236 none CN(C)C(=O)C#CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 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: [5, 4, 5, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 90, 120, 188, 188, 188, 188, 188, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 20, 90, 90, 188] 193
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277236 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277236
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277236/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277236
Building REAL300025277237
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277237'
/scratch/stefan/7808390/working/building/REAL300025277237 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277237

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277237/0 /scratch/stefan/7808390/working/building/REAL300025277237 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/93
`/scratch/stefan/7808390/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#C[C@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277237 none C#C[C@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 3, 10, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 61, 91, 182, 182, 182, 182, 182, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 19, 61, 61, 182] 201
rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277237 none C#C[C@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 10, 10, 10, 10, 10, 10, 22, 39, 39, 39, 95, 123, 201, 201, 201, 201, 201, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 39, 95, 95, 201] 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, 41, 42, 43, 44])
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: REAL300025277237 none C#C[C@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 201, 182, 191, 182, 182, 182, 182, 158, 182, 92, 92, 33, 92, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 182, 182, 182, 182, 182, 182, 182, 158, 158, 92, 33, 33, 1] 201
rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 761
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277237 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277237
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277237/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277237
Building REAL300025277238
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277238'
/scratch/stefan/7808390/working/building/REAL300025277238 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277238

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277238/0 /scratch/stefan/7808390/working/building/REAL300025277238 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/94
`/scratch/stefan/7808390/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)[N-]C1=O)

`REAL300025277238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277238 none CN1N=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)[N-]C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [12, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 31, 61, 151, 151, 151, 151, 151, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 31, 31, 151] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 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])
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: REAL300025277238 none CN1N=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)[N-]C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 9, 9, 12, 12, 12, 12, 12, 12, 21, 41, 41, 41, 107, 163, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 41, 107, 107, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277238 none CN1N=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)[N-]C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 151, 151, 151, 151, 151, 151, 151, 132, 151, 106, 106, 35, 106, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 151, 151, 151, 151, 132, 132, 106, 35, 35, 1] 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])
total number of confs: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277238 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277238
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277238/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277238
Building REAL300025277239
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277239'
/scratch/stefan/7808390/working/building/REAL300025277239 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277239

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277239/0 /scratch/stefan/7808390/working/building/REAL300025277239 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/95
`/scratch/stefan/7808390/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSCCC#N)

`REAL300025277239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277239 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSCCC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 86, 57, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 170, 187, 201, 201, 201, 126, 126, 126, 86, 86, 57, 29, 29, 1, 126, 126, 126, 126, 126, 126, 170, 170, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277239 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSCCC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 23, 37, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 2, 2, 4, 9, 22, 22, 22, 2, 2, 2, 3, 3, 6, 23, 23, 126, 1, 1, 1, 1, 1, 1, 4, 4, 22, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277239 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277239
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277239/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277239
Building REAL300025277240
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277240'
/scratch/stefan/7808390/working/building/REAL300025277240 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277240

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277240/0 /scratch/stefan/7808390/working/building/REAL300025277240 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/96
`/scratch/stefan/7808390/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1)

`REAL300025277240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277240 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [161, 121, 77, 77, 32, 77, 13, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 161, 161, 161, 121, 121, 77, 32, 32, 1, 161, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 791
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277240 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 4, 8, 8, 8, 32, 56, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 3, 3, 10, 10, 23, 23, 23, 23, 2, 2, 2, 4, 4, 8, 32, 32, 161, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277240 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NC=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 35, 57, 57, 57, 124, 147, 201, 201, 201, 201, 201, 17, 17, 17, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 35, 35, 57, 124, 124, 201, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277240 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277240
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277240/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277240
Building REAL300025277241
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277241'
/scratch/stefan/7808390/working/building/REAL300025277241 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277241

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277241/0 /scratch/stefan/7808390/working/building/REAL300025277241 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/97
`/scratch/stefan/7808390/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)N[C@@H](C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277241 none CNC(=O)N[C@@H](C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 130, 172, 172, 128, 130, 128, 128, 128, 128, 86, 128, 48, 48, 27, 48, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 172, 172, 172, 128, 128, 128, 128, 128, 128, 128, 128, 128, 86, 86, 48, 27, 27, 1] 201
rigid atoms, others: [50, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 881
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277241 none CNC(=O)N[C@@H](C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 11, 11, 11, 6, 4, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 32, 45, 128, 128, 128, 128, 128, 18, 18, 18, 18, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 10, 32, 32, 128] 201
rigid atoms, others: [36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277241 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277241
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277241/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277241
Building REAL300025277242
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277242'
/scratch/stefan/7808390/working/building/REAL300025277242 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277242

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277242/0 /scratch/stefan/7808390/working/building/REAL300025277242 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/98
`/scratch/stefan/7808390/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)OC)

`REAL300025277242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277242 none CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)OC 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 192, 146, 142, 146, 142, 142, 142, 142, 104, 142, 58, 58, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 198, 201, 201, 201, 201, 201, 201, 198, 192, 192, 142, 142, 142, 142, 142, 142, 142, 142, 142, 104, 104, 58, 31, 31, 1, 201, 201, 201] 201
rigid atoms, others: [48, 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, 49, 50, 51])
total number of confs: 896
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277242 none CCC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)OC 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 12, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 34, 47, 142, 142, 142, 142, 142, 12, 13, 13, 13, 13, 13, 13, 12, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 34, 34, 142, 13, 13, 13] 201
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 344
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277242 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277242
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277242/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277242
Building REAL300025277243
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277243'
/scratch/stefan/7808390/working/building/REAL300025277243 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277243

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277243/0 /scratch/stefan/7808390/working/building/REAL300025277243 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/99
`/scratch/stefan/7808390/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1)

`REAL300025277243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277243 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [149, 111, 65, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 184, 184, 201, 201, 201, 201, 201, 201, 149, 149, 149, 111, 111, 65, 30, 30, 1, 149, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 759
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277243 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 12, 12, 12, 41, 60, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 2, 2, 2, 6, 6, 12, 41, 41, 149, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277243 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 41, 41, 41, 110, 132, 201, 201, 201, 201, 201, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 41, 110, 110, 201, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 1] 201
rigid atoms, others: [42, 43, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/7808390/working/building/REAL300025277243 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277243
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277243/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277243
Building REAL300025277244
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277244'
/scratch/stefan/7808390/working/building/REAL300025277244 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277244

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277244/0 /scratch/stefan/7808390/working/building/REAL300025277244 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/100
`/scratch/stefan/7808390/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=N1)

`REAL300025277244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277244 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [168, 143, 96, 96, 34, 96, 13, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 174, 174, 178, 178, 178, 178, 168, 168, 168, 143, 143, 96, 34, 34, 1, 168, 168, 168, 168, 168, 168, 178, 178] 178
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 667
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277244 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 20, 20, 20, 72, 94, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 2, 2, 2, 6, 6, 20, 72, 72, 168, 1, 1, 1, 1, 1, 1, 9, 9] 178
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41])
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: REAL300025277244 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 18, 51, 51, 51, 117, 136, 178, 178, 178, 178, 178, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 51, 117, 117, 178, 9, 9, 9, 9, 9, 9, 1, 1] 178
rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 557
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277244 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277244
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277244/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277244
Building REAL300025277245
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277245'
/scratch/stefan/7808390/working/building/REAL300025277245 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277245

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277245/0 /scratch/stefan/7808390/working/building/REAL300025277245 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/101
`/scratch/stefan/7808390/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCOC1=O)

`REAL300025277245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277245 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCOC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 12, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [148, 119, 70, 70, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 148, 148, 148, 119, 119, 70, 28, 28, 1, 148, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 831
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277245 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCOC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 12, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 6, 12, 12, 12, 38, 60, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 2, 2, 8, 13, 13, 13, 13, 13, 2, 2, 2, 6, 6, 12, 38, 38, 148, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277245 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCOC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 12, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [13, 13, 13, 26, 44, 44, 44, 109, 133, 201, 201, 201, 201, 201, 13, 13, 13, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 44, 109, 109, 201, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277245 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277245
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277245/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277245
Building REAL300025277246
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277246'
/scratch/stefan/7808390/working/building/REAL300025277246 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277246

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277246/0 /scratch/stefan/7808390/working/building/REAL300025277246 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/102
`/scratch/stefan/7808390/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(CC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277246 none CC=C(CC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 118, 152, 201, 117, 118, 117, 117, 117, 117, 101, 117, 73, 73, 33, 73, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 117, 117, 117, 101, 101, 73, 33, 33, 1] 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])
total number of confs: 876
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277246 none CC=C(CC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 8, 13, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 47, 57, 117, 117, 117, 117, 117, 8, 8, 8, 8, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 47, 47, 117] 201
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 331
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277246 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277246
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277246/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277246
Building REAL300025277247
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277247'
/scratch/stefan/7808390/working/building/REAL300025277247 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277247

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277247/0 /scratch/stefan/7808390/working/building/REAL300025277247 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/103
`/scratch/stefan/7808390/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(F)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1)

`REAL300025277247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277247 none CC1=C(F)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', '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, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 36, 53, 134, 134, 134, 134, 134, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 36, 36, 134, 14] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 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])
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: REAL300025277247 none CC1=C(F)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', '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, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 26, 50, 50, 50, 124, 146, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 26, 26, 50, 124, 124, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 26] set([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])
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: REAL300025277247 none CC1=C(F)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', '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, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [201, 201, 201, 201, 164, 134, 164, 134, 134, 134, 134, 99, 134, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 134, 134, 134, 134, 99, 99, 56, 29, 29, 1, 201] 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])
total number of confs: 708
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277247 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277247
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277247/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277247
Building REAL300025277248
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277248'
/scratch/stefan/7808390/working/building/REAL300025277248 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277248

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277248/0 /scratch/stefan/7808390/working/building/REAL300025277248 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/104
`/scratch/stefan/7808390/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC12CC(C1)C2)

`REAL300025277248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277248 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC12CC(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [137, 100, 70, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 201, 201, 201, 201, 201, 137, 137, 137, 100, 100, 70, 29, 29, 1, 137, 137, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277248 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC12CC(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 26, 42, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 2, 2, 2, 3, 3, 6, 26, 26, 137, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277248 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC12CC(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 41, 41, 41, 109, 131, 201, 201, 201, 201, 201, 19, 19, 19, 19, 6, 19, 1, 1, 1, 1, 1, 1, 19, 19, 19, 27, 27, 41, 109, 109, 201, 19, 19, 19, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 615
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277248 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277248
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277248/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277248
Building REAL300025277249
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277249'
/scratch/stefan/7808390/working/building/REAL300025277249 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277249

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277249/0 /scratch/stefan/7808390/working/building/REAL300025277249 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/105
`/scratch/stefan/7808390/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCC(CC#C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277249 none C#CCC(CC#C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [177, 177, 139, 98, 139, 169, 169, 98, 98, 98, 98, 98, 98, 73, 98, 43, 43, 27, 43, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 139, 169, 169, 169, 98, 98, 98, 98, 98, 98, 98, 98, 98, 73, 73, 43, 27, 27, 1] 201
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 1019
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277249 none C#CCC(CC#C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 2, 4, 10, 10, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 22, 31, 98, 98, 98, 98, 98, 10, 10, 10, 4, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 22, 22, 98] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 263
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277249 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277249
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277249/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277249
Building REAL300025277250
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277250'
/scratch/stefan/7808390/working/building/REAL300025277250 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277250

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277250/0 /scratch/stefan/7808390/working/building/REAL300025277250 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/106
`/scratch/stefan/7808390/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)O)

`REAL300025277250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277250 none CCC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
294  conformations in input
total number of sets (complete confs): 294
using faster count positions algorithm for large data
unique positions, atoms: [89, 95, 75, 74, 75, 74, 74, 74, 74, 68, 74, 48, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 95, 98, 98, 97, 97, 97, 97, 97, 95, 74, 74, 74, 74, 74, 74, 74, 74, 74, 68, 68, 48, 28, 28, 1, 98, 98, 98, 98, 294] 294
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])
total number of confs: 784
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277250 none CCC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
294  conformations in input
total number of sets (complete confs): 294
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 32, 36, 74, 74, 74, 74, 74, 6, 10, 10, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 32, 32, 74, 10, 10, 10, 10, 30] 294
rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 37] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 274
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277250 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277250
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277250/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277250
Building REAL300025277251
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277251'
/scratch/stefan/7808390/working/building/REAL300025277251 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277251

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277251/0 /scratch/stefan/7808390/working/building/REAL300025277251 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/107
`/scratch/stefan/7808390/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277251 none COC(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 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, 8, 7, 8, 7, 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
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])
total number of confs: 12
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277251 none COC(F)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 7, 7, 8] 8
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277251 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277251
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277251/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277251
Building REAL300025277252
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277252'
/scratch/stefan/7808390/working/building/REAL300025277252 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277252

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277252/0 /scratch/stefan/7808390/working/building/REAL300025277252 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/108
`/scratch/stefan/7808390/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C#N)=CC1CC1)

`REAL300025277252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277252 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C#N)=CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.1', 'N.1', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 100, 66, 66, 32, 66, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 152, 152, 197, 197, 197, 197, 201, 201, 147, 147, 147, 100, 100, 66, 32, 32, 1, 147, 147, 147, 147, 147, 147, 197, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 795
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277252 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C#N)=CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.1', 'N.1', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 23, 39, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 15, 15, 2, 2, 2, 4, 4, 6, 23, 23, 147, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 300
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: REAL300025277252 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C#N)=CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.1', 'N.1', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 36, 36, 36, 98, 125, 201, 201, 201, 201, 201, 15, 15, 15, 14, 4, 14, 4, 4, 4, 1, 1, 1, 1, 15, 15, 15, 25, 25, 36, 98, 98, 201, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 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, 42])
total number of confs: 582
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277252 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277252
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277252/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277252
Building REAL300025277253
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277253'
/scratch/stefan/7808390/working/building/REAL300025277253 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277253

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277253/0 /scratch/stefan/7808390/working/building/REAL300025277253 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/109
`/scratch/stefan/7808390/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)ON=C1)

`REAL300025277253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277253 none CCC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)ON=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 32, 44, 120, 120, 120, 120, 120, 7, 7, 7, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 32, 32, 120, 7] 201
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277253 none CCC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)ON=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 5, 5, 7, 7, 7, 7, 7, 7, 13, 25, 25, 25, 66, 80, 141, 141, 141, 141, 141, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 25, 66, 66, 141, 1] 201
rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 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])
total number of confs: 399
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277253 none CCC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)ON=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 141, 141, 123, 120, 123, 120, 120, 120, 120, 90, 120, 47, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 120, 120, 120, 120, 90, 90, 47, 28, 28, 1, 141] 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])
total number of confs: 888
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277253 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277253
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277253/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277253
Building REAL300025277254
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277254'
/scratch/stefan/7808390/working/building/REAL300025277254 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277254

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277254/0 /scratch/stefan/7808390/working/building/REAL300025277254 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/110
`/scratch/stefan/7808390/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CS(N)(=O)=O)

`REAL300025277254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277254 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CS(N)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [95, 81, 45, 45, 21, 45, 12, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 175, 201, 201, 201, 95, 95, 95, 81, 81, 45, 21, 21, 1, 95, 95, 95, 95, 95, 95, 175, 175, 201, 201] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 905
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277254 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CS(N)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [1, 1, 1, 3, 9, 9, 9, 41, 41, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 3, 3, 9, 31, 31, 31, 2, 2, 2, 3, 3, 9, 41, 41, 95, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277254 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277254
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277254/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277254
Building REAL300025277255
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277255'
/scratch/stefan/7808390/working/building/REAL300025277255 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277255

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277255/0 /scratch/stefan/7808390/working/building/REAL300025277255 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/111
`/scratch/stefan/7808390/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1)

`REAL300025277255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277255 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens 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, 103, 60, 60, 28, 60, 12, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 179, 179, 201, 201, 201, 201, 201, 201, 145, 145, 145, 103, 103, 60, 28, 28, 1, 145, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277255 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 11, 11, 11, 38, 54, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 2, 2, 2, 6, 6, 11, 38, 38, 145, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277255 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens 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, 43, 43, 43, 115, 138, 201, 201, 201, 201, 201, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 43, 115, 115, 201, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 611
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277255 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277255
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277255/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277255
Building REAL300025277256
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277256'
/scratch/stefan/7808390/working/building/REAL300025277256 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277256

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277256/0 /scratch/stefan/7808390/working/building/REAL300025277256 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/112
`/scratch/stefan/7808390/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=C1CCCC1)

`REAL300025277256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277256 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 101, 53, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 142, 142, 201, 201, 201, 201, 201, 139, 139, 139, 101, 101, 53, 29, 29, 1, 139, 139, 139, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 785
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277256 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 30, 41, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 2, 2, 2, 5, 5, 9, 30, 30, 139, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277256 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 45, 45, 109, 126, 201, 201, 201, 201, 201, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 45, 109, 109, 201, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 603
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277256 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277256
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277256/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277256
Building REAL300025277257
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277257'
/scratch/stefan/7808390/working/building/REAL300025277257 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277257

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277257/0 /scratch/stefan/7808390/working/building/REAL300025277257 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/113
`/scratch/stefan/7808390/working/3D/113' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C#N)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277257 none CC(C)(C#N)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 201, 201, 100, 99, 100, 99, 99, 99, 99, 84, 99, 50, 50, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 137, 137, 99, 99, 99, 99, 99, 99, 99, 99, 99, 84, 84, 50, 25, 25, 1] 201
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])
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: REAL300025277257 none CC(C)(C#N)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 18, 18, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 39, 41, 99, 99, 99, 99, 99, 18, 18, 18, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 39, 39, 99] 201
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277257 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277257
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277257/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277257
Building REAL300025277258
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277258'
/scratch/stefan/7808390/working/building/REAL300025277258 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277258

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277258/0 /scratch/stefan/7808390/working/building/REAL300025277258 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/114
`/scratch/stefan/7808390/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(=O)NC1CC1)

`REAL300025277258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277258 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(=O)NC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 119, 77, 77, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 188, 201, 201, 201, 201, 201, 156, 156, 156, 119, 119, 77, 30, 30, 1, 156, 156, 156, 156, 156, 156, 188, 188, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277258 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(=O)NC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 33, 57, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 29, 29, 2, 2, 2, 5, 5, 9, 33, 33, 156, 1, 1, 1, 1, 1, 1, 5, 5, 10, 29, 29, 29, 29, 29] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([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, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 389
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277258 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC(=O)NC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 41, 54, 54, 54, 117, 146, 201, 201, 201, 201, 201, 29, 29, 29, 29, 22, 29, 6, 6, 6, 1, 1, 1, 1, 29, 29, 29, 41, 41, 54, 117, 117, 201, 29, 29, 29, 29, 29, 29, 22, 22, 6, 1, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 49, 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, 42, 43, 44])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277258 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277258
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277258/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277258
Building REAL300025277259
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277259'
/scratch/stefan/7808390/working/building/REAL300025277259 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277259

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277259/0 /scratch/stefan/7808390/working/building/REAL300025277259 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/115
`/scratch/stefan/7808390/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277259 none COCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 192, 152, 192, 147, 152, 147, 147, 147, 147, 120, 147, 80, 80, 32, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 576, 147, 147, 147, 147, 147, 147, 147, 147, 147, 120, 120, 80, 32, 32, 1] 603
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])
total number of confs: 1447
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277259 none COCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [26, 11, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 30, 51, 147, 147, 147, 147, 147, 26, 26, 26, 11, 11, 6, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 30, 30, 147] 603
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 367
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277259 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277259
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277259/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277259
Building REAL300025277260
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277260'
/scratch/stefan/7808390/working/building/REAL300025277260 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277260

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277260/0 /scratch/stefan/7808390/working/building/REAL300025277260 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/116
`/scratch/stefan/7808390/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CCCO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277260 none CC(C)(CCCO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [196, 196, 196, 196, 201, 201, 201, 191, 196, 191, 191, 191, 191, 158, 191, 79, 79, 33, 79, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 196, 201, 201, 201, 201, 201, 201, 603, 191, 191, 191, 191, 191, 191, 191, 191, 191, 158, 158, 79, 33, 33, 1] 603
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 1387
number of broken/clashed sets: 603
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277260 none CC(C)(CCCO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 6, 6, 12, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 54, 83, 191, 191, 191, 191, 191, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 12, 12, 36, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 19, 54, 54, 191] 603
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 522
number of broken/clashed sets: 603
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277260 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277260
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277260/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277260
Building REAL300025277261
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277261'
/scratch/stefan/7808390/working/building/REAL300025277261 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277261

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277261/0 /scratch/stefan/7808390/working/building/REAL300025277261 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/117
`/scratch/stefan/7808390/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CCOC1)

`REAL300025277261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277261 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need 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, 181, 200, 181, 181, 181, 181, 134, 181, 74, 74, 32, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 181, 181, 181, 181, 181, 134, 134, 74, 32, 32, 1, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [45, 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, 44, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 779
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277261 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 48, 71, 181, 181, 181, 181, 181, 7, 11, 11, 11, 11, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 48, 48, 181, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 36, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 428
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277261 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need 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, 11, 11, 11, 11, 11, 11, 22, 52, 52, 52, 115, 137, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 52, 115, 115, 201, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 597
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277261 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277261
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277261/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277261
Building REAL300025277262
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277262'
/scratch/stefan/7808390/working/building/REAL300025277262 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277262

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277262/0 /scratch/stefan/7808390/working/building/REAL300025277262 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/118
`/scratch/stefan/7808390/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(Cl)=C1)

`REAL300025277262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277262 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [131, 103, 74, 74, 31, 74, 13, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 139, 139, 200, 200, 200, 200, 200, 131, 131, 131, 103, 103, 74, 31, 31, 1, 131, 131, 131, 131, 131, 131, 200, 200] 200
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 637
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277262 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 14, 14, 14, 49, 59, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 2, 2, 2, 5, 5, 14, 49, 49, 131, 1, 1, 1, 1, 1, 1, 13, 13] 200
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 325
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: REAL300025277262 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 28, 64, 64, 64, 137, 154, 200, 200, 200, 200, 200, 13, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 64, 137, 137, 200, 13, 13, 13, 13, 13, 13, 1, 1] 200
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 637
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277262 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277262
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277262/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277262
Building REAL300025277263
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277263'
/scratch/stefan/7808390/working/building/REAL300025277263 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277263

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277263/0 /scratch/stefan/7808390/working/building/REAL300025277263 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/119
`/scratch/stefan/7808390/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)[C@H]1C[C@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277263 none C[NH+](C)[C@H]1C[C@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 7, 8, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 7, 7, 10, 3, 3] 10
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277263 none C[NH+](C)[C@H]1C[C@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 5, 7, 8, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 5, 7, 7, 10, 1, 1] 10
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 53, 54, 36, 29, 37] set([0, 2, 3, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277263 none C[NH+](C)[C@H]1C[C@H](C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 1, 10, 10] 10
rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54])
total number of confs: 26
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277263 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277263
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277263/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277263
Building REAL300025277264
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277264'
/scratch/stefan/7808390/working/building/REAL300025277264 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277264

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277264/0 /scratch/stefan/7808390/working/building/REAL300025277264 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/120
`/scratch/stefan/7808390/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C2CC2)CC1)

`REAL300025277264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277264 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C2CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 39, 39, 26, 39, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 174, 193, 201, 201, 193, 193, 94, 94, 94, 61, 61, 39, 26, 26, 1, 94, 94, 94, 94, 94, 94, 174, 174, 201, 201, 201, 201, 201, 193, 193, 193, 193] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 873
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.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: REAL300025277264 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C2CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 57, 57, 57, 107, 129, 201, 201, 201, 201, 201, 21, 21, 21, 21, 11, 21, 7, 1, 1, 1, 1, 7, 7, 21, 21, 21, 34, 34, 57, 107, 107, 201, 21, 21, 21, 21, 21, 21, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [44, 45, 46, 47, 48, 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, 42, 43, 49, 50, 51, 52])
total number of confs: 644
number of broken/clashed sets: 5
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277264 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C2CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 20, 28, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 7, 13, 21, 21, 13, 13, 2, 2, 2, 4, 4, 8, 20, 20, 94, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 13, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 252
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: REAL300025277264 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C2CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 43, 43, 43, 88, 110, 193, 193, 193, 193, 193, 13, 13, 13, 13, 5, 13, 1, 1, 1, 7, 7, 1, 1, 13, 13, 13, 23, 23, 43, 88, 88, 193, 13, 13, 13, 13, 13, 13, 5, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [49, 50, 51, 20, 21, 22, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 578
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277264 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277264
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277264/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277264
Building REAL300025277265
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277265'
/scratch/stefan/7808390/working/building/REAL300025277265 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277265

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277265/0 /scratch/stefan/7808390/working/building/REAL300025277265 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/121
`/scratch/stefan/7808390/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC1(F)F)

`REAL300025277265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277265 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC1(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [87, 73, 53, 53, 27, 53, 11, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 100, 100, 100, 100, 100, 87, 87, 87, 73, 73, 53, 27, 27, 1, 87, 87, 87, 87, 87, 87, 100, 100] 100
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025277265 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC1(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 14, 14, 14, 44, 52, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 14, 44, 44, 87, 1, 1, 1, 1, 1, 1, 6, 6] 100
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([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, 41, 42])
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: REAL300025277265 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC1(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [6, 6, 6, 15, 33, 33, 33, 70, 78, 100, 100, 100, 100, 100, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 33, 70, 70, 100, 6, 6, 6, 6, 6, 6, 1, 1] 100
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 330
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277265 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277265
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277265/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277265
Building REAL300025277266
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277266'
/scratch/stefan/7808390/working/building/REAL300025277266 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277266

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277266/0 /scratch/stefan/7808390/working/building/REAL300025277266 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/122
`/scratch/stefan/7808390/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1C#N)

`REAL300025277266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277266 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 122, 80, 80, 33, 80, 12, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 151, 151, 201, 201, 201, 201, 201, 201, 150, 150, 150, 122, 122, 80, 33, 33, 1, 150, 150, 150, 150, 150, 150, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 761
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277266 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 60, 73, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 15, 60, 60, 150, 1, 1, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
total number of confs: 382
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277266 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 22, 56, 56, 56, 138, 157, 201, 201, 201, 201, 201, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 56, 138, 138, 201, 9, 9, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277266 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277266
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277266/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277266
Building REAL300025277267
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277267'
/scratch/stefan/7808390/working/building/REAL300025277267 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277267

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277267/0 /scratch/stefan/7808390/working/building/REAL300025277267 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/123
`/scratch/stefan/7808390/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(CC)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277267 none CCCC(CC)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 180, 195, 195, 83, 83, 83, 83, 83, 83, 83, 59, 83, 39, 39, 27, 39, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 180, 180, 83, 83, 83, 83, 83, 83, 83, 83, 83, 59, 59, 39, 27, 27, 1] 201
rigid atoms, others: [56, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 880
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277267 none CCCC(CC)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 8, 15, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 21, 28, 83, 83, 83, 83, 83, 25, 25, 25, 25, 25, 25, 25, 15, 20, 20, 20, 20, 20, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 21, 21, 83] 201
rigid atoms, others: [45, 43, 7, 15, 9, 42, 11, 12, 13, 46, 44, 14, 47, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 327
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277267 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277267
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277267/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277267
Building REAL300025277268
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277268'
/scratch/stefan/7808390/working/building/REAL300025277268 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277268

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277268/0 /scratch/stefan/7808390/working/building/REAL300025277268 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/124
`/scratch/stefan/7808390/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277268 none C=C(C)CCCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 162, 138, 63, 63, 63, 63, 63, 63, 63, 44, 63, 36, 36, 25, 36, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 166, 166, 138, 138, 63, 63, 63, 63, 63, 63, 63, 63, 63, 44, 44, 36, 25, 25, 1] 201
rigid atoms, others: [51, 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, 50])
total number of confs: 976
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277268 none C=C(C)CCCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 17, 24, 63, 63, 63, 63, 63, 26, 26, 26, 26, 26, 13, 13, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 17, 17, 63] 201
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277268 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277268
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277268/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277268
Building REAL300025277269
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277269'
/scratch/stefan/7808390/working/building/REAL300025277269 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277269

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277269/0 /scratch/stefan/7808390/working/building/REAL300025277269 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/125
`/scratch/stefan/7808390/working/3D/125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1C)

`REAL300025277269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277269 none CC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 28, 37, 107, 107, 107, 107, 107, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 28, 28, 107, 17, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 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])
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: REAL300025277269 none CC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 17, 17, 17, 33, 57, 57, 57, 128, 144, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 57, 128, 128, 201, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 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: 678
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277269 none CC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 128, 107, 128, 107, 107, 107, 107, 81, 107, 45, 45, 26, 45, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 107, 107, 107, 107, 107, 107, 107, 107, 107, 81, 81, 45, 26, 26, 1, 201, 201, 201] 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])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277269 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277269
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277269/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277269
Building REAL300025277270
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277270'
/scratch/stefan/7808390/working/building/REAL300025277270 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277270

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277270/0 /scratch/stefan/7808390/working/building/REAL300025277270 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/126
`/scratch/stefan/7808390/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1C[C@@H](O)C1)

`REAL300025277270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277270 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [150, 117, 58, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 156, 156, 201, 201, 201, 201, 201, 201, 150, 150, 150, 117, 117, 58, 29, 29, 1, 150, 150, 150, 150, 150, 150, 201, 201, 603, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1413
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277270 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 6, 13, 13, 13, 42, 59, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 2, 6, 6, 13, 42, 42, 150, 1, 1, 1, 1, 1, 1, 11, 11, 33, 11, 11] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
total number of confs: 382
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277270 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [11, 11, 11, 27, 49, 49, 49, 118, 140, 201, 201, 201, 201, 201, 11, 11, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 27, 27, 49, 118, 118, 201, 11, 11, 11, 11, 11, 11, 1, 1, 3, 1, 1] 603
rigid atoms, others: [42, 43, 45, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277270 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277270
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277270/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277270
Building REAL300025277271
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277271'
/scratch/stefan/7808390/working/building/REAL300025277271 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277271

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277271/0 /scratch/stefan/7808390/working/building/REAL300025277271 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/127
`/scratch/stefan/7808390/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277271 none CC1(C)CC1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 22, 30, 96, 96, 96, 96, 96, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 22, 22, 96] 201
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277271 none CC1(C)CC1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 24, 24, 25, 25, 25, 25, 25, 25, 41, 64, 64, 64, 125, 143, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 41, 41, 64, 125, 125, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 5] 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, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277271 none CC1(C)CC1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 97, 96, 97, 96, 96, 96, 96, 67, 96, 40, 40, 24, 40, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 96, 96, 96, 96, 96, 96, 96, 96, 96, 67, 67, 40, 24, 24, 1] 201
rigid atoms, others: [51, 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, 50])
total number of confs: 874
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277271 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277271
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277271/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277271
Building REAL300025277272
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277272'
/scratch/stefan/7808390/working/building/REAL300025277272 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277272

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277272/0 /scratch/stefan/7808390/working/building/REAL300025277272 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/128
`/scratch/stefan/7808390/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)(C)C)

`REAL300025277272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277272 none CC(=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 145, 139, 145, 139, 139, 139, 139, 102, 139, 56, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 139, 139, 139, 139, 102, 102, 56, 31, 31, 1, 201, 201, 201, 201, 201, 201, 201, 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, 52, 53, 54])
total number of confs: 802
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277272 none CC(=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 34, 49, 139, 139, 139, 139, 139, 11, 15, 15, 15, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 34, 34, 139, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 334
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277272 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277272
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277272/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277272
Building REAL300025277273
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277273'
/scratch/stefan/7808390/working/building/REAL300025277273 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277273

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277273/0 /scratch/stefan/7808390/working/building/REAL300025277273 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/129
`/scratch/stefan/7808390/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CC1)

`REAL300025277273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277273 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [89, 74, 53, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 93, 93, 115, 115, 115, 115, 89, 89, 89, 74, 74, 53, 29, 29, 1, 89, 89, 89, 89, 89, 89, 115, 115, 115, 115] 115
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025277273 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 39, 45, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 2, 2, 2, 5, 5, 12, 39, 39, 89, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 115
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277273 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 27, 52, 52, 52, 91, 100, 115, 115, 115, 115, 115, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 52, 91, 91, 115, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 115
rigid atoms, others: [40, 41, 42, 43, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 406
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277273 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277273
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277273/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277273
Building REAL300025277274
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277274'
/scratch/stefan/7808390/working/building/REAL300025277274 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277274

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277274/0 /scratch/stefan/7808390/working/building/REAL300025277274 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/130
`/scratch/stefan/7808390/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=NN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277274 none CC1=NN=NN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 57, 88, 178, 178, 178, 178, 178, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 57, 57, 178] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277274 none CC1=NN=NN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 8, 8, 10, 10, 10, 10, 10, 10, 23, 39, 39, 39, 108, 138, 201, 201, 201, 201, 201, 2, 2, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 39, 108, 108, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277274 none CC1=NN=NN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 182, 178, 182, 178, 178, 178, 178, 155, 178, 88, 88, 31, 88, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 178, 178, 178, 178, 178, 178, 178, 178, 178, 155, 155, 88, 31, 31, 1] 201
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 789
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277274 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277274
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277274/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277274
Building REAL300025277275
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277275'
/scratch/stefan/7808390/working/building/REAL300025277275 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277275

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277275/0 /scratch/stefan/7808390/working/building/REAL300025277275 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/131
`/scratch/stefan/7808390/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2)

`REAL300025277275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277275 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [65, 62, 53, 53, 28, 53, 12, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 66, 66, 66, 66, 66, 66, 66, 65, 65, 65, 62, 62, 53, 28, 28, 1, 65, 65, 65, 65, 65, 65, 66, 66, 66, 66] 66
rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277275 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 41, 47, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 15, 41, 41, 65, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 66
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277275 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 8, 18, 18, 18, 44, 50, 66, 66, 66, 66, 66, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 18, 44, 44, 66, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 66
rigid atoms, others: [43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 205
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277275 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277275
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277275/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277275
Building REAL300025277276
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277276'
/scratch/stefan/7808390/working/building/REAL300025277276 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277276

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277276/0 /scratch/stefan/7808390/working/building/REAL300025277276 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/132
`/scratch/stefan/7808390/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(=O)O1)

`REAL300025277276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277276 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [126, 102, 72, 72, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 129, 129, 134, 134, 134, 134, 134, 126, 126, 126, 102, 102, 72, 31, 31, 1, 126, 126, 126, 126, 126, 126, 134, 134] 134
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025277276 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 16, 16, 16, 59, 75, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 2, 2, 2, 5, 5, 16, 59, 59, 126, 1, 1, 1, 1, 1, 1, 11, 11] 134
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277276 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(=O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 22, 47, 47, 47, 101, 111, 134, 134, 134, 134, 134, 11, 11, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 22, 22, 47, 101, 101, 134, 11, 11, 11, 11, 11, 11, 1, 1] 134
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 451
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277276 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277276
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277276/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277276
Building REAL300025277277
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277277'
/scratch/stefan/7808390/working/building/REAL300025277277 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277277

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277277/0 /scratch/stefan/7808390/working/building/REAL300025277277 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/133
`/scratch/stefan/7808390/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277277 none CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 10, 18, 10, 10, 10, 2, 10, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 33, 48, 132, 132, 132, 132, 132, 18, 18, 18, 18, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 33, 33, 132] 201
rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277277 none CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 10, 10, 10, 10, 10, 10, 19, 38, 38, 38, 107, 129, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 38, 107, 107, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277277 none CC(C)[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 134, 201, 132, 134, 132, 132, 132, 132, 93, 132, 52, 52, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 132, 132, 132, 132, 93, 93, 52, 29, 29, 1] 201
rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/7808390/working/building/REAL300025277277 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277277
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277277/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277277
Building REAL300025277278
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277278'
/scratch/stefan/7808390/working/building/REAL300025277278 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277278

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277278/0 /scratch/stefan/7808390/working/building/REAL300025277278 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/134
`/scratch/stefan/7808390/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(Cl)=N1)

`REAL300025277278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277278 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [186, 147, 95, 95, 36, 95, 13, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 200, 200, 201, 201, 201, 201, 201, 186, 186, 186, 147, 147, 95, 36, 36, 1, 186, 186, 186, 186, 186, 186, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 759
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277278 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 20, 20, 20, 75, 101, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 20, 75, 75, 186, 1, 1, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 468
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277278 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 21, 58, 58, 58, 130, 159, 201, 201, 201, 201, 201, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 58, 130, 130, 201, 8, 8, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277278 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277278/1 /scratch/stefan/7808390/working/building/REAL300025277278 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/135
`/scratch/stefan/7808390/working/3D/135' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(Cl)N1)

`REAL300025277278.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277278/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277278 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(Cl)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [39, 34, 27, 27, 18, 27, 11, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 34, 34, 27, 18, 18, 1, 39, 39, 39, 39, 39, 39, 40, 40] 40
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 139
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277278 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(Cl)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 3, 10, 10, 10, 24, 26, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 2, 2, 2, 3, 3, 10, 24, 24, 39, 1, 1, 1, 1, 1, 1, 7, 7] 40
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 130
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: REAL300025277278 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(Cl)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 12, 22, 22, 22, 35, 36, 40, 40, 40, 40, 40, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 22, 35, 35, 40, 7, 7, 7, 7, 7, 7, 1, 1] 40
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 149
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277278 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277278
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277278/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277278/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277278
Building REAL300025277279
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277279'
/scratch/stefan/7808390/working/building/REAL300025277279 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277279

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277279/0 /scratch/stefan/7808390/working/building/REAL300025277279 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/136
`/scratch/stefan/7808390/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC2CCCC12)

`REAL300025277279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277279 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC2CCCC12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 72, 44, 44, 25, 44, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 126, 126, 201, 201, 201, 201, 201, 201, 106, 106, 106, 72, 72, 44, 25, 25, 1, 106, 106, 106, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 623
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277279 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC2CCCC12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 27, 37, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 3, 3, 13, 12, 13, 13, 13, 13, 2, 2, 2, 5, 5, 9, 27, 27, 106, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277279 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC2CCCC12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 54, 54, 54, 119, 136, 201, 201, 201, 201, 201, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 54, 119, 119, 201, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/7808390/working/building/REAL300025277279 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277279
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277279/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277279
Building REAL300025277280
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277280'
/scratch/stefan/7808390/working/building/REAL300025277280 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277280

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277280/0 /scratch/stefan/7808390/working/building/REAL300025277280 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/137
`/scratch/stefan/7808390/working/3D/137' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277280 none CCN1N=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 35, 43, 124, 124, 124, 124, 124, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 35, 35, 124] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277280 none CCN1N=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 3, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 70, 82, 152, 152, 152, 152, 152, 6, 6, 6, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 70, 70, 152] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 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, 46, 47])
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: REAL300025277280 none CCN1N=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need 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, 152, 127, 124, 127, 124, 124, 124, 124, 87, 124, 44, 44, 24, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 152, 124, 124, 124, 124, 124, 124, 124, 124, 124, 87, 87, 44, 24, 24, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 853
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277280 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277280
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277280/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277280
Building REAL300025277281
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277281'
/scratch/stefan/7808390/working/building/REAL300025277281 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277281

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277281/0 /scratch/stefan/7808390/working/building/REAL300025277281 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/138
`/scratch/stefan/7808390/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COCCO)

`REAL300025277281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277281 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COCCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [158, 119, 84, 84, 32, 84, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 158, 161, 198, 201, 201, 158, 158, 158, 119, 119, 84, 32, 32, 1, 158, 158, 158, 158, 158, 158, 161, 161, 201, 201, 201, 201, 603] 603
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1309
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: REAL300025277281 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COCCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 3, 7, 7, 7, 32, 56, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 2, 2, 3, 8, 15, 24, 2, 2, 2, 3, 3, 7, 32, 32, 158, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 24, 24, 72] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 478
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277281 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277281
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277281/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277281
Building REAL300025277282
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277282'
/scratch/stefan/7808390/working/building/REAL300025277282 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277282

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277282/0 /scratch/stefan/7808390/working/building/REAL300025277282 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/139
`/scratch/stefan/7808390/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1)

`REAL300025277282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277282 none CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 43, 67, 158, 158, 158, 158, 158, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 12, 43, 43, 158] 201
rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277282 none CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 27, 52, 52, 52, 123, 146, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 52, 123, 123, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 25, 26] set([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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277282 none CC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [201, 201, 201, 201, 163, 158, 163, 158, 158, 158, 158, 123, 158, 66, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 158, 158, 158, 158, 158, 123, 123, 66, 30, 30, 1] 201
rigid atoms, others: [49, 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])
total number of confs: 695
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277282 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277282
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277282/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277282
Building REAL300025277283
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277283'
/scratch/stefan/7808390/working/building/REAL300025277283 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277283

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277283/0 /scratch/stefan/7808390/working/building/REAL300025277283 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/140
`/scratch/stefan/7808390/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NC=C(F)C=N1)

`REAL300025277283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277283 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NC=C(F)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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: [147, 112, 65, 65, 31, 65, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 185, 185, 201, 201, 201, 201, 201, 201, 147, 147, 147, 112, 112, 65, 31, 31, 1, 147, 147, 147, 147, 147, 147, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025277283 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NC=C(F)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 5, 11, 11, 11, 39, 56, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 4, 4, 11, 11, 4, 6, 11, 11, 2, 2, 2, 5, 5, 11, 39, 39, 147, 1, 1, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277283 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NC=C(F)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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: [12, 12, 12, 26, 47, 47, 47, 112, 132, 201, 201, 201, 201, 201, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 47, 112, 112, 201, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277283 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277283
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277283/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277283
Building REAL300025277284
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277284'
/scratch/stefan/7808390/working/building/REAL300025277284 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277284

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277284/0 /scratch/stefan/7808390/working/building/REAL300025277284 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/141
`/scratch/stefan/7808390/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277284 none CC(C)[C@@H](O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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, 183, 201, 168, 183, 183, 128, 128, 128, 128, 128, 128, 128, 92, 128, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 549, 168, 168, 128, 128, 128, 128, 128, 128, 128, 128, 128, 92, 92, 48, 29, 29, 1] 603
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 1497
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277284 none CC(C)[C@@H](O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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: [23, 11, 23, 6, 11, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 32, 42, 128, 128, 128, 128, 128, 23, 23, 23, 23, 23, 23, 23, 33, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 32, 32, 128] 603
rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277284 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277284
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277284/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277284
Building REAL300025277285
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277285'
/scratch/stefan/7808390/working/building/REAL300025277285 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277285

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277285/0 /scratch/stefan/7808390/working/building/REAL300025277285 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/142
`/scratch/stefan/7808390/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277285 none C=CCC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 181, 117, 181, 117, 117, 117, 117, 117, 117, 82, 117, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 181, 181, 117, 117, 117, 117, 117, 117, 117, 117, 117, 82, 82, 53, 28, 28, 1] 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])
total number of confs: 918
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277285 none C=CCC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 22, 34, 117, 117, 117, 117, 117, 21, 21, 21, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 22, 22, 117] 201
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277285 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277285
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277285/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277285
Building REAL300025277286
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277286'
/scratch/stefan/7808390/working/building/REAL300025277286 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277286

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277286/0 /scratch/stefan/7808390/working/building/REAL300025277286 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/143
`/scratch/stefan/7808390/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1)

`REAL300025277286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277286 none CC1CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 51, 73, 169, 169, 169, 169, 169, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 14, 51, 51, 169] 201
rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277286 none CC1CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 10, 10, 10, 10, 10, 10, 19, 41, 41, 41, 102, 127, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 41, 102, 102, 201] 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: 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: REAL300025277286 none CC1CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 173, 169, 173, 169, 169, 169, 169, 132, 169, 67, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169, 169, 169, 169, 169, 169, 132, 132, 67, 30, 30, 1] 201
rigid atoms, others: [49, 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])
total number of confs: 796
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277286 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277286
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277286/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277286
Building REAL300025277287
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277287'
/scratch/stefan/7808390/working/building/REAL300025277287 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277287

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277287/0 /scratch/stefan/7808390/working/building/REAL300025277287 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/144
`/scratch/stefan/7808390/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277287 none CC1CCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 71, 80, 122, 122, 122, 122, 122, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 20, 71, 71, 122] 123
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 359
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: REAL300025277287 none CC1CCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 9, 23, 23, 23, 73, 82, 123, 123, 123, 123, 123, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 23, 73, 73, 123] 123
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 360
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: REAL300025277287 none CC1CCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 123, 123, 123, 122, 123, 122, 122, 122, 122, 115, 122, 68, 68, 32, 68, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 122, 122, 122, 122, 122, 122, 122, 122, 122, 115, 115, 68, 32, 32, 1] 123
rigid atoms, others: [51, 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, 50])
total number of confs: 474
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277287 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277287
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277287/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277287
Building REAL300025277288
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277288'
/scratch/stefan/7808390/working/building/REAL300025277288 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277288

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277288/0 /scratch/stefan/7808390/working/building/REAL300025277288 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/145
`/scratch/stefan/7808390/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2C3CC1CC32)

`REAL300025277288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277288 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2C3CC1CC32 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 59, 47, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 59, 59, 47, 27, 27, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60] 60
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277288 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2C3CC1CC32 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 39, 46, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 15, 39, 39, 60, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 60
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277288 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C2C3CC1CC32 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 8, 19, 19, 19, 42, 47, 60, 60, 60, 60, 60, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 42, 42, 60, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 191
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277288 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277288
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277288/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277288
Building REAL300025277289
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277289'
/scratch/stefan/7808390/working/building/REAL300025277289 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277289

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277289/0 /scratch/stefan/7808390/working/building/REAL300025277289 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/146
`/scratch/stefan/7808390/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H](O)C1CCCC1)

`REAL300025277289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277289 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H](O)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [131, 93, 53, 53, 27, 53, 12, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 141, 141, 187, 187, 187, 201, 201, 201, 201, 131, 131, 131, 93, 93, 53, 27, 27, 1, 131, 131, 131, 131, 131, 131, 561, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603
rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1441
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: REAL300025277289 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H](O)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 5, 10, 10, 10, 33, 45, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 17, 17, 17, 17, 2, 2, 2, 5, 5, 10, 33, 33, 131, 1, 1, 1, 1, 1, 1, 30, 17, 17, 17, 17, 17, 17, 17, 17, 17] 603
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 353
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277289 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H](O)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 17, 33, 55, 55, 55, 111, 124, 201, 201, 201, 201, 201, 17, 17, 17, 15, 5, 15, 1, 5, 5, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 55, 111, 111, 201, 17, 17, 17, 17, 17, 17, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 659
number of broken/clashed sets: 105
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277289 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277289
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277289/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277289
Building REAL300025277290
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277290'
/scratch/stefan/7808390/working/building/REAL300025277290 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277290

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277290/0 /scratch/stefan/7808390/working/building/REAL300025277290 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/147
`/scratch/stefan/7808390/working/3D/147' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277290 none CNC(=O)NC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 130, 172, 128, 130, 128, 128, 128, 128, 86, 128, 48, 48, 27, 48, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 172, 172, 172, 172, 128, 128, 128, 128, 128, 128, 128, 128, 128, 86, 86, 48, 27, 27, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 881
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277290 none CNC(=O)NC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 11, 11, 11, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 32, 45, 128, 128, 128, 128, 128, 18, 18, 18, 18, 11, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 10, 32, 32, 128] 201
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277290 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277290
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277290/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277290
Building REAL300025277291
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277291'
/scratch/stefan/7808390/working/building/REAL300025277291 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277291

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277291/0 /scratch/stefan/7808390/working/building/REAL300025277291 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/148
`/scratch/stefan/7808390/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277291 none CCN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 45, 60, 135, 135, 135, 135, 135, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 45, 45, 135] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277291 none CCN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need 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, 5, 5, 5, 5, 5, 5, 13, 25, 25, 25, 69, 83, 145, 145, 145, 145, 145, 3, 3, 3, 3, 3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 25, 69, 69, 145] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 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, 46, 47])
total number of confs: 416
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277291 none CCN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need 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, 135, 135, 135, 135, 135, 135, 135, 108, 135, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 135, 135, 135, 135, 135, 135, 135, 135, 135, 108, 108, 53, 28, 28, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 883
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277291 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277291
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277291/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277291
Building REAL300025277292
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277292'
/scratch/stefan/7808390/working/building/REAL300025277292 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277292

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277292/0 /scratch/stefan/7808390/working/building/REAL300025277292 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/149
`/scratch/stefan/7808390/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1(C2CCC2)CC1)

`REAL300025277292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277292 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1(C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 92, 52, 52, 27, 52, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 123, 123, 153, 201, 201, 201, 153, 153, 116, 116, 116, 92, 92, 52, 27, 27, 1, 116, 116, 116, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 780
number of broken/clashed sets: 1
./output.2.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: REAL300025277292 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1(C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 46, 46, 46, 103, 127, 201, 201, 201, 201, 201, 11, 11, 11, 10, 8, 10, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 23, 23, 46, 103, 103, 201, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 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, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52])
total number of confs: 615
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277292 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1(C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 38, 53, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 3, 3, 4, 11, 11, 11, 4, 4, 2, 2, 2, 5, 5, 13, 38, 38, 116, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 293
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: REAL300025277292 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1(C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 21, 21, 21, 58, 79, 153, 153, 153, 153, 153, 4, 4, 4, 3, 1, 3, 1, 1, 8, 8, 8, 1, 1, 4, 4, 4, 10, 10, 21, 58, 58, 153, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [50, 49, 18, 51, 20, 21, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 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: 400
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277292 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277292
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277292/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277292
Building REAL300025277293
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277293'
/scratch/stefan/7808390/working/building/REAL300025277293 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277293

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277293/0 /scratch/stefan/7808390/working/building/REAL300025277293 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/150
`/scratch/stefan/7808390/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21)

`REAL300025277293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277293 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 103, 74, 74, 29, 74, 11, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 103, 103, 74, 29, 29, 1, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108] 108
rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277293 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 20, 20, 20, 66, 75, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 7, 7, 20, 66, 66, 108, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 108
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49])
total number of confs: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277293 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 11, 26, 26, 26, 73, 83, 108, 108, 108, 108, 108, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 26, 73, 73, 108, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 108
rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 333
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277293 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277293
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277293/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277293
Building REAL300025277294
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277294'
/scratch/stefan/7808390/working/building/REAL300025277294 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277294

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277294/0 /scratch/stefan/7808390/working/building/REAL300025277294 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/151
`/scratch/stefan/7808390/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N1)

`REAL300025277294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277294 none CCC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 19, 29, 98, 98, 98, 98, 98, 9, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 19, 19, 98, 9] 201
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 251
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277294 none CCC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 8, 8, 9, 9, 9, 9, 9, 9, 14, 19, 19, 19, 46, 62, 161, 161, 161, 161, 161, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 19, 46, 46, 161, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 26] set([0, 7, 8, 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, 47, 48])
total number of confs: 380
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: REAL300025277294 none CCC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 161, 161, 161, 161, 119, 98, 119, 98, 98, 98, 98, 75, 98, 51, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 201, 201, 161, 161, 98, 98, 98, 98, 98, 98, 98, 98, 98, 75, 75, 51, 28, 28, 1, 161] 201
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])
total number of confs: 783
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277294 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277294
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277294/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277294
Building REAL300025277295
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277295'
/scratch/stefan/7808390/working/building/REAL300025277295 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277295

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277295/0 /scratch/stefan/7808390/working/building/REAL300025277295 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/152
`/scratch/stefan/7808390/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C#CC1CCCO1)

`REAL300025277295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277295 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C#CC1CCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 62, 48, 48, 25, 48, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 62, 62, 48, 25, 25, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66] 66
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 244
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277295 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C#CC1CCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 14, 14, 14, 40, 47, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 14, 40, 40, 66, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 66
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 205
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: REAL300025277295 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C#CC1CCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 7, 16, 16, 16, 41, 48, 66, 66, 66, 66, 66, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 16, 41, 41, 66, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1] 66
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 187
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277295 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277295
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277295/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277295
Building REAL300025277296
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277296'
/scratch/stefan/7808390/working/building/REAL300025277296 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277296

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277296/0 /scratch/stefan/7808390/working/building/REAL300025277296 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/153
`/scratch/stefan/7808390/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277296 none C[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [8, 8, 8, 8, 2, 8, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 53, 63, 123, 123, 123, 123, 123, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 13, 53, 53, 123] 164
rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: REAL300025277296 none C[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 19, 46, 46, 46, 107, 119, 164, 164, 164, 164, 164, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 46, 107, 107, 164] 164
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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, 44, 45])
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: REAL300025277296 none C[C@@H]1C[C@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 164, 164, 123, 164, 123, 123, 123, 123, 123, 123, 100, 123, 69, 69, 31, 69, 12, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 123, 123, 123, 123, 123, 123, 123, 123, 123, 100, 100, 69, 31, 31, 1] 164
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])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277296 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277296
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277296/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277296
Building REAL300025277297
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277297'
/scratch/stefan/7808390/working/building/REAL300025277297 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277297

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277297/0 /scratch/stefan/7808390/working/building/REAL300025277297 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/154
`/scratch/stefan/7808390/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCCCC1)

`REAL300025277297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277297 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 20, 20, 16, 20, 10, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 26, 28, 28, 28, 28, 28, 28, 23, 23, 23, 23, 23, 20, 16, 16, 1, 23, 23, 23, 23, 23, 23, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28
rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277297 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
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, 4, 8, 8, 8, 14, 17, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 8, 14, 14, 23, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 28
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277297 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 10, 10, 10, 17, 20, 28, 28, 28, 28, 28, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 10, 17, 17, 28, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28
rigid atoms, others: [54, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 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, 43, 44])
total number of confs: 91
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277297 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277297/1 /scratch/stefan/7808390/working/building/REAL300025277297 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/155
`/scratch/stefan/7808390/working/3D/155' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCCCC1)

`REAL300025277297.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277297/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277297 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 114, 70, 70, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 168, 168, 201, 201, 201, 201, 201, 201, 153, 153, 153, 114, 114, 70, 28, 28, 1, 153, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 831
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277297 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 38, 55, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 4, 4, 10, 14, 14, 14, 14, 14, 2, 2, 2, 5, 5, 10, 38, 38, 153, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277297 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 43, 43, 43, 105, 128, 201, 201, 201, 201, 201, 14, 14, 14, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 43, 105, 105, 201, 14, 14, 14, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 613
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277297 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277297
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277297/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277297/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277297
Building REAL300025277298
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277298'
/scratch/stefan/7808390/working/building/REAL300025277298 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277298

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277298/0 /scratch/stefan/7808390/working/building/REAL300025277298 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/156
`/scratch/stefan/7808390/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277298 none C[N@@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 4, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 6, 2, 2] 6
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 27
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277298 none C[N@@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 6, 1, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 35, 53, 54, 36, 33, 27, 37, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277298 none C[N@@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 6, 6, 6, 6, 5, 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, 6, 6, 6, 6, 6, 1, 6, 6] 6
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54])
total number of confs: 12
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277298 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277298/1 /scratch/stefan/7808390/working/building/REAL300025277298 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/157
`/scratch/stefan/7808390/working/3D/157' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277298.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277298/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277298 none C[N@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 17, 19, 31, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 17, 17, 31, 3, 3] 32
rigid atoms, others: [43, 38, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 104
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277298 none C[N@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11, 18, 20, 32, 32, 32, 32, 32, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 11, 18, 18, 32, 1, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 53, 54, 36, 33, 27, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 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: 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: REAL300025277298 none C[N@H+]1CCCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 31, 31, 31, 31, 31, 31, 31, 31, 31, 25, 25, 20, 25, 10, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 25, 20, 20, 1, 32, 32] 32
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54])
total number of confs: 123
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277298 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277298
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277298/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277298/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277298
Building REAL300025277299
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277299'
/scratch/stefan/7808390/working/building/REAL300025277299 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277299

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277299/0 /scratch/stefan/7808390/working/building/REAL300025277299 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/158
`/scratch/stefan/7808390/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C[N+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1)

`REAL300025277299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277299 none CN1C=C[N+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.cat', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 4, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 8, 3] 9
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277299 none CN1C=C[N+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.cat', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 9, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 49, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277299 none CN1C=C[N+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.cat', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 9] 9
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])
total number of confs: 20
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277299 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277299
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277299/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277299
Building REAL300025277300
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277300'
/scratch/stefan/7808390/working/building/REAL300025277300 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277300

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277300/0 /scratch/stefan/7808390/working/building/REAL300025277300 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/159
`/scratch/stefan/7808390/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277300 none CC1=NC=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 37, 54, 145, 145, 145, 145, 145, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 37, 37, 145] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277300 none CC1=NC=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 11, 23, 43, 43, 43, 107, 130, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 43, 107, 107, 201] 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])
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: REAL300025277300 none CC1=NC=CN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 170, 145, 170, 145, 145, 145, 145, 113, 145, 62, 62, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 145, 145, 145, 145, 113, 113, 62, 31, 31, 1] 201
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 729
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277300 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277300
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277300/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277300
Building REAL300025277301
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277301'
/scratch/stefan/7808390/working/building/REAL300025277301 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277301

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277301/0 /scratch/stefan/7808390/working/building/REAL300025277301 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/160
`/scratch/stefan/7808390/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOCC1)

`REAL300025277301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277301 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [68, 59, 46, 46, 23, 46, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 70, 70, 70, 70, 68, 68, 68, 59, 59, 46, 23, 23, 1, 68, 68, 68, 68, 68, 68, 70, 70, 70, 70] 70
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277301 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 40, 49, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 2, 2, 2, 5, 5, 15, 40, 40, 68, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 70
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277301 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 19, 34, 34, 34, 52, 58, 70, 70, 70, 70, 70, 10, 10, 10, 9, 1, 9, 1, 1, 1, 1, 1, 10, 10, 10, 19, 19, 34, 52, 52, 70, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 70
rigid atoms, others: [40, 41, 42, 43, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 220
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277301 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277301
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277301/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277301
Building REAL300025277302
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277302'
/scratch/stefan/7808390/working/building/REAL300025277302 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277302

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277302/0 /scratch/stefan/7808390/working/building/REAL300025277302 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/161
`/scratch/stefan/7808390/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1=NOC=C1)

`REAL300025277302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277302 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 101, 71, 71, 31, 71, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 177, 201, 201, 201, 201, 201, 130, 130, 130, 101, 101, 71, 31, 31, 1, 130, 130, 130, 130, 130, 130, 177, 177, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 778
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277302 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 6, 6, 6, 25, 40, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 2, 2, 8, 18, 27, 27, 27, 27, 2, 2, 2, 3, 3, 6, 25, 25, 130, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277302 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 37, 45, 45, 45, 103, 130, 201, 201, 201, 201, 201, 27, 27, 27, 26, 14, 26, 3, 1, 1, 1, 1, 1, 1, 27, 27, 27, 37, 37, 45, 103, 103, 201, 27, 27, 27, 27, 27, 27, 14, 14, 1, 1] 201
rigid atoms, others: [44, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277302 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277302
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277302/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277302
Building REAL300025277303
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277303'
/scratch/stefan/7808390/working/building/REAL300025277303 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277303

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277303/0 /scratch/stefan/7808390/working/building/REAL300025277303 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/162
`/scratch/stefan/7808390/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1C)

`REAL300025277303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277303 none CC1=COC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1C 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 40, 56, 144, 144, 144, 144, 144, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 40, 40, 144, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277303 none CC1=COC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1C 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 11, 11, 11, 11, 11, 11, 24, 46, 46, 46, 114, 136, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 46, 114, 114, 201, 2, 2, 2] 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, 46, 47, 48])
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: REAL300025277303 none CC1=COC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1C 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 163, 144, 163, 144, 144, 144, 144, 105, 144, 56, 56, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 144, 144, 144, 144, 144, 105, 105, 56, 27, 27, 1, 201, 201, 201] 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])
total number of confs: 701
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277303 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277303
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277303/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277303
Building REAL300025277304
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277304'
/scratch/stefan/7808390/working/building/REAL300025277304 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277304

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277304/0 /scratch/stefan/7808390/working/building/REAL300025277304 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/163
`/scratch/stefan/7808390/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CC=N1)

`REAL300025277304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277304 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 88, 61, 61, 30, 61, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 130, 130, 197, 201, 201, 201, 201, 201, 116, 116, 116, 88, 88, 61, 30, 30, 1, 116, 116, 116, 116, 116, 116, 197, 197, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277304 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 8, 8, 8, 32, 44, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 4, 4, 12, 19, 19, 19, 19, 19, 2, 2, 2, 3, 3, 8, 32, 32, 116, 1, 1, 1, 1, 1, 1, 12, 12, 19, 19, 19] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277304 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 28, 46, 46, 46, 101, 111, 201, 201, 201, 201, 201, 19, 19, 19, 16, 8, 16, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 28, 28, 46, 101, 101, 201, 19, 19, 19, 19, 19, 19, 8, 8, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 590
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277304 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277304
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277304/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277304
Building REAL300025277305
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277305'
/scratch/stefan/7808390/working/building/REAL300025277305 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277305

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277305/0 /scratch/stefan/7808390/working/building/REAL300025277305 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/164
`/scratch/stefan/7808390/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277305 none CC(C#N)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 108, 107, 108, 107, 107, 107, 107, 87, 107, 54, 54, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 191, 191, 107, 107, 107, 107, 107, 107, 107, 107, 107, 87, 87, 54, 25, 25, 1] 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])
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: REAL300025277305 none CC(C#N)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 40, 42, 107, 107, 107, 107, 107, 20, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 40, 40, 107] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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
/scratch/stefan/7808390/working/building/REAL300025277305 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277305
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277305/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277305
Building REAL300025277306
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277306'
/scratch/stefan/7808390/working/building/REAL300025277306 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277306

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277306/0 /scratch/stefan/7808390/working/building/REAL300025277306 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/165
`/scratch/stefan/7808390/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1)

`REAL300025277306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277306 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens 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, 103, 60, 60, 28, 60, 12, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 179, 179, 201, 201, 201, 201, 201, 201, 145, 145, 145, 103, 103, 60, 28, 28, 1, 145, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277306 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 11, 11, 11, 38, 54, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 2, 2, 2, 6, 6, 11, 38, 38, 145, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277306 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(N)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens 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, 43, 43, 43, 115, 138, 201, 201, 201, 201, 201, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 43, 115, 115, 201, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 611
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277306 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277306
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277306/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277306
Building REAL300025277307
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277307'
/scratch/stefan/7808390/working/building/REAL300025277307 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277307

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277307/0 /scratch/stefan/7808390/working/building/REAL300025277307 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/166
`/scratch/stefan/7808390/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1OCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277307 none CCC1OCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 33, 45, 148, 148, 148, 148, 148, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 33, 33, 148] 201
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277307 none CCC1OCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 9, 9, 9, 9, 20, 41, 41, 41, 94, 113, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 41, 94, 94, 201] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 568
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277307 none CCC1OCCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 165, 148, 165, 148, 148, 148, 148, 98, 148, 49, 49, 28, 49, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148, 148, 148, 148, 148, 148, 148, 148, 98, 98, 49, 28, 28, 1] 201
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 802
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277307 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277307
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277307/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277307
Building REAL300025277308
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277308'
/scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277308

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277308/0 /scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/167
`/scratch/stefan/7808390/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1)

`REAL300025277308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none C[N@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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, 37, 45, 35, 35, 35, 35, 35, 35, 35, 34, 35, 29, 29, 23, 29, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 37, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 34, 29, 23, 23, 1, 45, 45, 45, 45, 45] 45
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, 51])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none C[N@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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, 6, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 16, 17, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 16, 16, 35, 9, 9, 9, 9, 9] 45
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none C[N@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 4, 8, 8, 9, 9, 9, 9, 9, 9, 11, 12, 12, 12, 24, 26, 45, 45, 45, 45, 45, 1, 1, 1, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 12, 24, 24, 45, 1, 1, 1, 1, 1] 45
rigid atoms, others: [1, 47, 48, 49, 50, 51, 24, 25, 26] set([0, 2, 3, 4, 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])
total number of confs: 130
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277308/1 /scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/168
`/scratch/stefan/7808390/working/3D/168' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1)

`REAL300025277308.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277308/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none C[N@@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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, 33, 39, 31, 31, 31, 31, 31, 31, 31, 30, 31, 28, 28, 20, 28, 11, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 33, 33, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 28, 20, 20, 1, 39, 39, 39, 39, 39] 39
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, 51])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none C[N@@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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: [11, 7, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 14, 16, 31, 31, 31, 31, 31, 11, 12, 12, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 14, 14, 31, 12, 12, 12, 12, 12] 39
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none C[N@@H+](CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 6, 11, 11, 12, 12, 12, 12, 12, 12, 14, 15, 15, 15, 25, 26, 39, 39, 39, 39, 39, 1, 1, 1, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 15, 25, 25, 39, 1, 1, 1, 1, 1] 39
rigid atoms, others: [1, 47, 48, 49, 50, 51, 24, 25, 26] set([0, 2, 3, 4, 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])
total number of confs: 128
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277308/2 /scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/169
`/scratch/stefan/7808390/working/3D/169' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1)

`REAL300025277308.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277308/2/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: REAL300025277308 none CN(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 10, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 157, 183, 157, 157, 157, 157, 121, 157, 72, 72, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 157, 157, 157, 157, 121, 121, 72, 30, 30, 1, 201, 201, 201, 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])
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: REAL300025277308 none CN(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 10, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 41, 68, 157, 157, 157, 157, 157, 13, 15, 15, 13, 13, 13, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 41, 41, 157, 15, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 378
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277308 none CN(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 10, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 5, 10, 10, 15, 15, 15, 15, 15, 15, 29, 47, 47, 47, 109, 144, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 47, 109, 109, 201, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 46, 47, 48, 49, 50, 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, 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: 626
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277308 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277308
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277308/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277308/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277308/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277308
Building REAL300025277309
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277309'
/scratch/stefan/7808390/working/building/REAL300025277309 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277309

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277309/0 /scratch/stefan/7808390/working/building/REAL300025277309 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/170
`/scratch/stefan/7808390/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277309 none CN1C=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 22, 31, 98, 98, 98, 98, 98, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 22, 22, 98] 201
rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277309 none CN1C=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 18, 18, 18, 18, 18, 18, 29, 47, 47, 47, 102, 121, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 47, 102, 102, 201] 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, 44, 45, 46, 47, 48, 49])
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: REAL300025277309 none CN1C=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 183, 104, 98, 104, 98, 98, 98, 98, 72, 98, 50, 50, 27, 50, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 183, 183, 98, 98, 98, 98, 98, 98, 98, 98, 98, 72, 72, 50, 27, 27, 1] 201
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 806
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277309 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277309
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277309/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277309
Building REAL300025277310
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277310'
/scratch/stefan/7808390/working/building/REAL300025277310 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277310

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277310/0 /scratch/stefan/7808390/working/building/REAL300025277310 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/171
`/scratch/stefan/7808390/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCOC1CC1)

`REAL300025277310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277310 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCOC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [132, 94, 76, 76, 32, 76, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 148, 155, 175, 201, 201, 132, 132, 132, 94, 94, 76, 32, 32, 1, 132, 132, 132, 132, 132, 132, 148, 148, 155, 155, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 783
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277310 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCOC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 3, 5, 5, 5, 24, 45, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 1, 2, 3, 7, 21, 21, 2, 2, 2, 3, 3, 5, 24, 24, 132, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 21, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 315
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277310 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCOC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [21, 21, 21, 28, 39, 39, 39, 116, 154, 201, 201, 201, 201, 201, 21, 21, 21, 21, 19, 21, 11, 6, 1, 1, 1, 1, 21, 21, 21, 28, 28, 39, 116, 116, 201, 21, 21, 21, 21, 21, 21, 19, 19, 11, 11, 1, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 49, 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, 41, 42, 43, 44])
total number of confs: 650
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277310 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277310
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277310/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277310
Building REAL300025277311
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277311'
/scratch/stefan/7808390/working/building/REAL300025277311 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277311

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277311/0 /scratch/stefan/7808390/working/building/REAL300025277311 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/172
`/scratch/stefan/7808390/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCCO)

`REAL300025277311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277311 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [95, 62, 47, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 176, 198, 201, 198, 201, 95, 95, 95, 62, 62, 47, 29, 29, 1, 95, 95, 95, 95, 95, 95, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 603] 603
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 1543
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277311 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 3, 6, 6, 6, 20, 30, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 2, 2, 8, 11, 13, 11, 23, 2, 2, 2, 3, 3, 6, 20, 20, 95, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 23, 23, 72] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 379
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277311 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277311
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277311/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277311
Building REAL300025277312
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277312'
/scratch/stefan/7808390/working/building/REAL300025277312 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277312

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277312/0 /scratch/stefan/7808390/working/building/REAL300025277312 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/173
`/scratch/stefan/7808390/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277312 none COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 6, 10, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 33, 47, 116, 116, 116, 116, 116, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 33, 33, 116] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277312 none COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 29, 29, 29, 72, 92, 158, 158, 158, 158, 158, 4, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 29, 72, 72, 158] 201
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277312 none COC(=O)[C@@H]1C[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 158, 158, 158, 116, 158, 116, 116, 116, 116, 116, 116, 88, 116, 55, 55, 26, 55, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 158, 158, 116, 116, 116, 116, 116, 116, 116, 116, 116, 88, 88, 55, 26, 26, 1] 201
rigid atoms, others: [48, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 771
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277312 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277312
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277312/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277312
Building REAL300025277313
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277313'
/scratch/stefan/7808390/working/building/REAL300025277313 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277313

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277313/0 /scratch/stefan/7808390/working/building/REAL300025277313 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/174
`/scratch/stefan/7808390/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CON=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277313 none CC1=CON=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 37, 52, 142, 142, 142, 142, 142, 18, 18, 18, 18, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 37, 37, 142] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277313 none CC1=CON=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 18, 18, 18, 18, 18, 18, 33, 50, 50, 50, 112, 132, 201, 201, 201, 201, 201, 2, 2, 2, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 33, 33, 50, 112, 112, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30] set([7, 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])
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: REAL300025277313 none CC1=CON=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 145, 142, 145, 142, 142, 142, 142, 111, 142, 54, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 198, 142, 142, 142, 142, 142, 142, 142, 142, 142, 111, 111, 54, 30, 30, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 859
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277313 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277313
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277313/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277313
Building REAL300025277314
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277314'
/scratch/stefan/7808390/working/building/REAL300025277314 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277314

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277314/0 /scratch/stefan/7808390/working/building/REAL300025277314 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/175
`/scratch/stefan/7808390/working/3D/175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1)

`REAL300025277314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277314 none C#CC1=CC=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 30, 40, 119, 119, 119, 119, 119, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 30, 30, 119, 10] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 263
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277314 none C#CC1=CC=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 10, 10, 10, 10, 10, 10, 22, 39, 39, 39, 95, 118, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 39, 95, 95, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 47, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 573
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: REAL300025277314 none C#CC1=CC=CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 126, 119, 126, 119, 119, 119, 119, 79, 119, 45, 45, 25, 45, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 119, 119, 119, 79, 79, 45, 25, 25, 1, 201] 201
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
total number of confs: 624
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277314 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277314
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277314/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277314
Building REAL300025277315
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277315'
/scratch/stefan/7808390/working/building/REAL300025277315 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277315

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277315/0 /scratch/stefan/7808390/working/building/REAL300025277315 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/176
`/scratch/stefan/7808390/working/3D/176' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277315 none CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 32, 46, 134, 134, 134, 134, 134, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 32, 32, 134] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277315 none CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 12, 22, 22, 22, 64, 81, 155, 155, 155, 155, 155, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 22, 64, 64, 155] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 26] set([0, 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: 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: REAL300025277315 none CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 155, 155, 155, 139, 134, 139, 134, 134, 134, 134, 97, 134, 55, 55, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 134, 134, 134, 134, 97, 97, 55, 28, 28, 1] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 850
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277315 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277315
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277315/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277315
Building REAL300025277316
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277316'
/scratch/stefan/7808390/working/building/REAL300025277316 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277316

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277316/0 /scratch/stefan/7808390/working/building/REAL300025277316 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/177
`/scratch/stefan/7808390/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C[NH+](C)C)

`REAL300025277316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277316 none CC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 9, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 1, 11, 11, 11, 11, 11, 11, 11, 11] 11
rigid atoms, others: [48, 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, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 32
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277316 none CC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 7, 7, 9, 5, 5, 5, 5, 5, 5, 5, 5] 11
rigid atoms, others: [34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 11, 35, 38, 37] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 54
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277316 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277316
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277316/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277316
Building REAL300025277317
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277317'
/scratch/stefan/7808390/working/building/REAL300025277317 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277317

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277317/0 /scratch/stefan/7808390/working/building/REAL300025277317 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/178
`/scratch/stefan/7808390/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=C(N)C=N1)

`REAL300025277317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277317 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [142, 110, 66, 66, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 147, 147, 188, 201, 201, 201, 201, 201, 142, 142, 142, 110, 110, 66, 27, 27, 1, 142, 142, 142, 142, 142, 142, 188, 188, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277317 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 4, 8, 8, 8, 34, 52, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 3, 3, 9, 17, 17, 17, 17, 17, 2, 2, 2, 4, 4, 8, 34, 34, 142, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
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: REAL300025277317 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [17, 17, 17, 27, 51, 51, 51, 116, 135, 201, 201, 201, 201, 201, 17, 17, 17, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 27, 27, 51, 116, 116, 201, 17, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277317 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277317
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277317/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277317
Building REAL300025277318
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277318'
/scratch/stefan/7808390/working/building/REAL300025277318 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277318

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277318/0 /scratch/stefan/7808390/working/building/REAL300025277318 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/179
`/scratch/stefan/7808390/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277318 none CC(CCO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [190, 144, 190, 201, 201, 140, 144, 140, 140, 140, 140, 98, 140, 50, 50, 26, 50, 12, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 201, 201, 201, 201, 603, 140, 140, 140, 140, 140, 140, 140, 140, 140, 98, 98, 50, 26, 26, 1] 603
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])
total number of confs: 1518
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277318 none CC(CCO)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 3, 5, 9, 17, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 31, 42, 140, 140, 140, 140, 140, 5, 5, 5, 5, 10, 10, 16, 17, 51, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 31, 31, 140] 603
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 403
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277318 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277318
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277318/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277318
Building REAL300025277319
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277319'
/scratch/stefan/7808390/working/building/REAL300025277319 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277319

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277319/0 /scratch/stefan/7808390/working/building/REAL300025277319 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/180
`/scratch/stefan/7808390/working/3D/180' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=CC1CC1)

`REAL300025277319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277319 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 99, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 149, 149, 189, 189, 189, 201, 201, 147, 147, 147, 99, 99, 53, 28, 28, 1, 147, 147, 147, 147, 147, 147, 189, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 803
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277319 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 28, 42, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 22, 22, 2, 2, 2, 4, 4, 8, 28, 28, 147, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 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: REAL300025277319 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)=CC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 67, 67, 67, 135, 151, 201, 201, 201, 201, 201, 22, 22, 22, 21, 7, 21, 7, 7, 1, 1, 1, 1, 22, 22, 22, 41, 41, 67, 135, 135, 201, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 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, 41])
total number of confs: 691
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277319 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277319
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277319/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277319
Building REAL300025277320
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277320'
/scratch/stefan/7808390/working/building/REAL300025277320 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277320

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277320/0 /scratch/stefan/7808390/working/building/REAL300025277320 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/181
`/scratch/stefan/7808390/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(F)C1)

`REAL300025277320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277320 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 76, 43, 43, 26, 43, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 188, 201, 201, 201, 201, 112, 112, 112, 76, 76, 43, 26, 26, 1, 112, 112, 112, 112, 112, 112, 188, 188, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277320 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 25, 33, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 2, 2, 8, 20, 20, 20, 20, 2, 2, 2, 4, 4, 8, 25, 25, 112, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 277
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277320 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 62, 62, 62, 125, 137, 201, 201, 201, 201, 201, 20, 20, 20, 20, 6, 20, 1, 1, 1, 1, 1, 1, 20, 20, 20, 37, 37, 62, 125, 125, 201, 20, 20, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/7808390/working/building/REAL300025277320 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277320
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277320/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277320
Building REAL300025277321
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277321'
/scratch/stefan/7808390/working/building/REAL300025277321 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277321

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277321/0 /scratch/stefan/7808390/working/building/REAL300025277321 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/182
`/scratch/stefan/7808390/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CCC1)

`REAL300025277321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277321 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 80, 49, 49, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 103, 127, 127, 163, 201, 201, 201, 103, 103, 103, 80, 80, 49, 25, 25, 1, 103, 103, 103, 103, 103, 103, 127, 163, 163, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277321 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 7, 23, 35, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 23, 23, 23, 2, 2, 2, 3, 3, 7, 23, 23, 103, 1, 1, 1, 1, 1, 1, 4, 13, 13, 23, 23, 23, 23, 23, 23, 23] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277321 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(F)CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 60, 60, 60, 119, 135, 201, 201, 201, 201, 201, 23, 23, 23, 23, 14, 23, 5, 14, 1, 1, 1, 1, 1, 23, 23, 23, 36, 36, 60, 119, 119, 201, 23, 23, 23, 23, 23, 23, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 676
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277321 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277321
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277321/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277321
Building REAL300025277322
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277322'
/scratch/stefan/7808390/working/building/REAL300025277322 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277322

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277322/0 /scratch/stefan/7808390/working/building/REAL300025277322 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/183
`/scratch/stefan/7808390/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H](O)CF)

`REAL300025277322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277322 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H](O)CF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [52, 42, 25, 25, 17, 25, 12, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 63, 63, 63, 63, 52, 52, 52, 42, 42, 25, 17, 17, 1, 52, 52, 52, 52, 52, 52, 189, 63, 63] 189
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 460
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: REAL300025277322 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H](O)CF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [1, 1, 1, 3, 9, 9, 9, 27, 27, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 15, 2, 2, 2, 3, 3, 9, 27, 27, 52, 1, 1, 1, 1, 1, 1, 21, 15, 15] 189
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 220
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277322 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277322
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277322/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277322
Building REAL300025277323
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277323'
/scratch/stefan/7808390/working/building/REAL300025277323 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277323

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277323/0 /scratch/stefan/7808390/working/building/REAL300025277323 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/184
`/scratch/stefan/7808390/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277323 none CCC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 14, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 17, 24, 83, 83, 83, 83, 83, 14, 23, 23, 23, 23, 23, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 17, 17, 83, 14, 14] 201
rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 233
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277323 none CCC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 12, 12, 14, 14, 14, 14, 14, 14, 25, 43, 43, 43, 84, 104, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 43, 84, 84, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 52, 26, 51] set([0, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 561
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: REAL300025277323 none CCC1(C)C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 102, 83, 102, 83, 83, 83, 83, 53, 83, 34, 34, 26, 34, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 83, 83, 83, 83, 83, 83, 53, 53, 34, 26, 26, 1, 201, 201] 201
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])
total number of confs: 563
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277323 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277323
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277323/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277323
Building REAL300025277324
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277324'
/scratch/stefan/7808390/working/building/REAL300025277324 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277324

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277324/0 /scratch/stefan/7808390/working/building/REAL300025277324 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/185
`/scratch/stefan/7808390/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277324 none CCC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 28, 38, 123, 123, 123, 123, 123, 7, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 28, 28, 123, 7, 7] 201
rigid atoms, others: [43, 6, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 289
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277324 none CCC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 16, 31, 31, 31, 78, 99, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 31, 78, 78, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 53, 54, 36, 26, 37] set([0, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 522
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: REAL300025277324 none CCC1(C)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 123, 123, 78, 123, 43, 43, 24, 43, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 123, 123, 123, 123, 78, 78, 43, 24, 24, 1, 201, 201] 201
rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] 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, 50, 51, 53, 54])
total number of confs: 759
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277324 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277324
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277324/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277324
Building REAL300025277325
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277325'
/scratch/stefan/7808390/working/building/REAL300025277325 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277325

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277325/0 /scratch/stefan/7808390/working/building/REAL300025277325 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/186
`/scratch/stefan/7808390/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277325 none CCN1C=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 34, 101, 101, 101, 101, 101, 9, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 24, 24, 101] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277325 none CCN1C=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 9, 9, 9, 9, 9, 9, 12, 24, 24, 24, 68, 90, 157, 157, 157, 157, 157, 1, 6, 6, 6, 6, 6, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 24, 68, 68, 157] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 445
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277325 none CCN1C=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 157, 157, 157, 101, 101, 101, 101, 101, 101, 101, 75, 101, 43, 43, 26, 43, 13, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 157, 101, 101, 101, 101, 101, 101, 101, 101, 101, 75, 75, 43, 26, 26, 1] 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])
total number of confs: 774
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277325 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277325
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277325/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277325
Building REAL300025277326
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277326'
/scratch/stefan/7808390/working/building/REAL300025277326 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277326

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277326/0 /scratch/stefan/7808390/working/building/REAL300025277326 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/187
`/scratch/stefan/7808390/working/3D/187' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277326 none CCCC(C)(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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, 175, 175, 175, 175, 144, 144, 144, 144, 144, 144, 144, 102, 144, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 525, 175, 175, 144, 144, 144, 144, 144, 144, 144, 144, 144, 102, 102, 58, 30, 30, 1] 603
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 1412
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277326 none CCCC(C)(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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, 6, 5, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 37, 54, 144, 144, 144, 144, 144, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 18, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 37, 37, 144] 603
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 391
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277326 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277326
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277326/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277326
Building REAL300025277327
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277327'
/scratch/stefan/7808390/working/building/REAL300025277327 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277327

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277327/0 /scratch/stefan/7808390/working/building/REAL300025277327 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/188
`/scratch/stefan/7808390/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(C#N)O1)

`REAL300025277327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277327 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(C#N)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 117, 54, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 176, 176, 201, 201, 201, 201, 201, 201, 156, 156, 156, 117, 117, 54, 30, 30, 1, 156, 156, 156, 156, 156, 156, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 753
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277327 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(C#N)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 15, 15, 15, 44, 57, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 2, 2, 2, 7, 7, 15, 44, 44, 156, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
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: REAL300025277327 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(C#N)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 25, 52, 52, 52, 130, 145, 201, 201, 201, 201, 201, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 25, 52, 130, 130, 201, 10, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 647
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277327 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277327
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277327/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277327
Building REAL300025277328
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277328'
/scratch/stefan/7808390/working/building/REAL300025277328 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277328

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277328/0 /scratch/stefan/7808390/working/building/REAL300025277328 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/189
`/scratch/stefan/7808390/working/3D/189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CC=N1)

`REAL300025277328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277328 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 93, 65, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 141, 141, 196, 201, 201, 201, 201, 201, 127, 127, 127, 93, 93, 65, 30, 30, 1, 127, 127, 127, 127, 127, 127, 196, 196, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 841
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277328 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 8, 8, 8, 31, 45, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 3, 3, 11, 18, 18, 18, 18, 18, 2, 2, 2, 3, 3, 8, 31, 31, 127, 1, 1, 1, 1, 1, 1, 11, 11, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 299
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: REAL300025277328 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 26, 42, 42, 42, 99, 113, 201, 201, 201, 201, 201, 18, 18, 18, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 26, 26, 42, 99, 99, 201, 18, 18, 18, 18, 18, 18, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 585
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277328 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277328
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277328/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277328
Building REAL300025277329
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277329'
/scratch/stefan/7808390/working/building/REAL300025277329 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277329

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277329/0 /scratch/stefan/7808390/working/building/REAL300025277329 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/190
`/scratch/stefan/7808390/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CC1)

`REAL300025277329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277329 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [41, 36, 25, 25, 15, 25, 11, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 46, 46, 48, 48, 41, 41, 41, 36, 36, 25, 15, 15, 1, 41, 41, 41, 41, 41, 41, 46, 138, 48, 48, 48, 48, 48] 144
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 322
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: REAL300025277329 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 8, 8, 8, 25, 25, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 3, 3, 6, 6, 13, 13, 2, 2, 2, 3, 3, 8, 25, 25, 41, 1, 1, 1, 1, 1, 1, 6, 18, 13, 13, 13, 13, 13] 144
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 181
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: REAL300025277329 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 20, 31, 31, 31, 44, 44, 48, 48, 48, 48, 48, 13, 13, 13, 13, 6, 13, 1, 6, 1, 1, 1, 13, 13, 13, 20, 20, 31, 44, 44, 48, 13, 13, 13, 13, 13, 13, 6, 18, 1, 1, 1, 1, 1] 144
rigid atoms, others: [42, 43, 44, 45, 46, 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, 41])
total number of confs: 224
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277329 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277329
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277329/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277329
Building REAL300025277330
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277330'
/scratch/stefan/7808390/working/building/REAL300025277330 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277330

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277330/0 /scratch/stefan/7808390/working/building/REAL300025277330 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/191
`/scratch/stefan/7808390/working/3D/191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=C1)

`REAL300025277330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277330 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [61, 53, 35, 35, 21, 35, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 62, 62, 77, 77, 77, 77, 77, 61, 61, 61, 53, 53, 35, 21, 21, 1, 61, 61, 61, 61, 61, 61, 77, 77, 77, 77] 77
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277330 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 34, 36, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 2, 2, 2, 3, 3, 11, 34, 34, 61, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9] 77
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277330 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [27, 27, 27, 43, 86, 86, 86, 131, 131, 151, 151, 151, 151, 151, 27, 27, 27, 24, 8, 24, 1, 1, 1, 1, 1, 1, 27, 27, 27, 43, 43, 86, 131, 131, 151, 27, 27, 27, 27, 27, 27, 8, 8, 1, 1] 151
rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 554
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277330 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277330
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277330/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277330
Building REAL300025277331
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277331'
/scratch/stefan/7808390/working/building/REAL300025277331 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277331

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277331/0 /scratch/stefan/7808390/working/building/REAL300025277331 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/192
`/scratch/stefan/7808390/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277331 none C=C(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 124, 124, 124, 124, 124, 124, 124, 100, 124, 59, 59, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 124, 124, 124, 124, 100, 100, 59, 27, 27, 1] 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])
total number of confs: 883
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277331 none C=C(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 43, 45, 124, 124, 124, 124, 124, 20, 20, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 43, 43, 124] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 332
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277331 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277331
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277331/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277331
Building REAL300025277332
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277332'
/scratch/stefan/7808390/working/building/REAL300025277332 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277332

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277332/0 /scratch/stefan/7808390/working/building/REAL300025277332 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/193
`/scratch/stefan/7808390/working/3D/193' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025277332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277332 none CC1=CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 42, 59, 120, 120, 120, 120, 120, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 14, 42, 42, 120, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277332 none CC1=CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 9, 9, 9, 18, 38, 38, 38, 95, 119, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 38, 95, 95, 201, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 49, 50, 51, 52, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 552
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277332 none CC1=CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 128, 120, 128, 120, 120, 120, 120, 83, 120, 55, 55, 29, 55, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 120, 120, 120, 120, 83, 83, 55, 29, 29, 1, 201, 201, 201, 201] 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: 785
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277332 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277332
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277332/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277332
Building REAL300025277333
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277333'
/scratch/stefan/7808390/working/building/REAL300025277333 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277333

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277333/0 /scratch/stefan/7808390/working/building/REAL300025277333 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/194
`/scratch/stefan/7808390/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277333 none CCSCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 142, 142, 142, 142, 142, 142, 142, 113, 142, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 142, 142, 142, 142, 142, 142, 142, 142, 142, 113, 113, 61, 29, 29, 1] 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])
total number of confs: 845
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277333 none CCSCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 31, 44, 142, 142, 142, 142, 142, 18, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 31, 31, 142] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277333 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277333
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277333/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277333
Building REAL300025277334
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277334'
/scratch/stefan/7808390/working/building/REAL300025277334 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277334

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277334/0 /scratch/stefan/7808390/working/building/REAL300025277334 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/195
`/scratch/stefan/7808390/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)OCCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277334 none CC(=O)OCCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 154, 147, 115, 115, 115, 115, 115, 115, 115, 92, 115, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 154, 147, 147, 115, 115, 115, 115, 115, 115, 115, 115, 115, 92, 92, 68, 30, 30, 1] 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])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277334 none CC(=O)OCCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 24, 37, 115, 115, 115, 115, 115, 15, 15, 15, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 24, 24, 115] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277334 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277334
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277334/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277334
Building REAL300025277335
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277335'
/scratch/stefan/7808390/working/building/REAL300025277335 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277335

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277335/0 /scratch/stefan/7808390/working/building/REAL300025277335 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/196
`/scratch/stefan/7808390/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277335 none CC(C)=C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 88, 109, 87, 88, 87, 87, 87, 87, 82, 87, 65, 65, 31, 65, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 109, 109, 109, 87, 87, 87, 87, 87, 87, 87, 87, 87, 82, 82, 65, 31, 31, 1] 109
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])
total number of confs: 409
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277335 none CC(C)=C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 45, 53, 87, 87, 87, 87, 87, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 45, 45, 87] 109
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 254
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277335 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277335
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277335/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277335
Building REAL300025277336
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277336'
/scratch/stefan/7808390/working/building/REAL300025277336 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277336

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277336/0 /scratch/stefan/7808390/working/building/REAL300025277336 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/197
`/scratch/stefan/7808390/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C=NS1)

`REAL300025277336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277336 none CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 71, 87, 157, 157, 157, 157, 157, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 18, 71, 71, 157, 6] 191
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 404
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: REAL300025277336 none CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 18, 49, 49, 49, 126, 145, 191, 191, 191, 191, 191, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 49, 126, 126, 191, 1] 191
rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 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])
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: REAL300025277336 none CC1=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 158, 157, 158, 157, 157, 157, 157, 131, 157, 83, 83, 34, 83, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 191, 157, 157, 157, 157, 157, 157, 157, 157, 157, 131, 131, 83, 34, 34, 1, 191] 191
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])
total number of confs: 673
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277336 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277336
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277336/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277336
Building REAL300025277337
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277337'
/scratch/stefan/7808390/working/building/REAL300025277337 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277337

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277337/0 /scratch/stefan/7808390/working/building/REAL300025277337 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/198
`/scratch/stefan/7808390/working/3D/198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1[O-])

`REAL300025277337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277337 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [177, 156, 125, 125, 47, 125, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 180, 180, 181, 181, 181, 181, 181, 181, 177, 177, 177, 156, 156, 125, 47, 47, 1, 177, 177, 177, 177, 177, 177, 181, 181, 181] 181
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 644
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: REAL300025277337 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 8, 8, 8, 44, 80, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 8, 44, 44, 177, 1, 1, 1, 1, 1, 1, 7, 7, 7] 181
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 378
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: REAL300025277337 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 12, 24, 24, 24, 78, 114, 181, 181, 181, 181, 181, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 24, 78, 78, 181, 7, 7, 7, 7, 7, 7, 1, 1, 1] 181
rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 472
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277337 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277337/1 /scratch/stefan/7808390/working/building/REAL300025277337 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/199
`/scratch/stefan/7808390/working/3D/199' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1O)

`REAL300025277337.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277337/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277337 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [63, 55, 43, 43, 26, 43, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 55, 55, 43, 26, 26, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63, 126] 126
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 360
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: REAL300025277337 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 36, 42, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 2, 2, 2, 5, 5, 13, 36, 36, 63, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10] 126
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 209
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: REAL300025277337 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 10, 21, 21, 21, 44, 49, 63, 63, 63, 63, 63, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 21, 44, 44, 63, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2] 126
rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45])
total number of confs: 208
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277337 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277337
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277337/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277337/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277337
Building REAL300025277338
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277338'
/scratch/stefan/7808390/working/building/REAL300025277338 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277338

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277338/0 /scratch/stefan/7808390/working/building/REAL300025277338 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/200
`/scratch/stefan/7808390/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=N1)

`REAL300025277338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277338 none CC1(CCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 25, 36, 110, 110, 110, 110, 110, 22, 22, 22, 22, 22, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 25, 25, 110] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36, 38, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 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: REAL300025277338 none CC1(CCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 8, 9, 22, 22, 22, 22, 22, 22, 22, 22, 36, 55, 55, 55, 109, 123, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 8, 8, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 55, 109, 109, 201] 201
rigid atoms, others: [0, 1, 2, 24, 25] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277338 none CC1(CCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 168, 161, 110, 110, 110, 110, 110, 110, 110, 77, 110, 50, 50, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 161, 161, 110, 110, 110, 110, 110, 110, 110, 110, 110, 77, 77, 50, 30, 30, 1] 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])
total number of confs: 876
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277338 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277338
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277338/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277338
Building REAL300025277339
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277339'
/scratch/stefan/7808390/working/building/REAL300025277339 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277339

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277339/0 /scratch/stefan/7808390/working/building/REAL300025277339 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/201
`/scratch/stefan/7808390/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)[N-]O1)

`REAL300025277339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277339 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [191, 170, 118, 118, 41, 118, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 200, 200, 201, 201, 201, 201, 201, 191, 191, 191, 170, 170, 118, 41, 41, 1, 191, 191, 191, 191, 191, 191, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277339 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 17, 17, 17, 70, 110, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 2, 2, 2, 7, 7, 17, 70, 70, 191, 1, 1, 1, 1, 1, 1, 11] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025277339 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 26, 51, 51, 51, 116, 148, 201, 201, 201, 201, 201, 11, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 51, 116, 116, 201, 11, 11, 11, 11, 11, 11, 1] 201
rigid atoms, others: [41, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 593
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277339 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277339
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277339/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277339
Building REAL300025277340
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277340'
/scratch/stefan/7808390/working/building/REAL300025277340 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277340

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277340/0 /scratch/stefan/7808390/working/building/REAL300025277340 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/202
`/scratch/stefan/7808390/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1COC1)

`REAL300025277340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277340 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [138, 100, 67, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 138, 162, 183, 201, 201, 201, 138, 138, 138, 100, 100, 67, 30, 30, 1, 138, 138, 138, 138, 138, 138, 162, 162, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 798
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277340 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 3, 6, 6, 6, 25, 41, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 2, 2, 5, 11, 25, 25, 25, 2, 2, 2, 3, 3, 6, 25, 25, 138, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277340 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)COC1COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [25, 25, 25, 35, 55, 55, 55, 110, 134, 201, 201, 201, 201, 201, 25, 25, 25, 25, 20, 25, 6, 1, 1, 1, 1, 1, 25, 25, 25, 35, 35, 55, 110, 110, 201, 25, 25, 25, 25, 25, 25, 20, 20, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/7808390/working/building/REAL300025277340 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277340
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277340/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277340
Building REAL300025277341
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277341'
/scratch/stefan/7808390/working/building/REAL300025277341 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277341

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277341/0 /scratch/stefan/7808390/working/building/REAL300025277341 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/203
`/scratch/stefan/7808390/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@]2(C(=O)N3CCCC3(C)CNC(=O)CSC3=NNC(=O)[N-]3)C[C@H]12)

`REAL300025277341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277341 none C[C@@H]1C[C@]2(C(=O)N3CCCC3(C)CNC(=O)CSC3=NNC(=O)[N-]3)C[C@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 67, 94, 159, 159, 159, 159, 159, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 21, 67, 67, 159, 9, 9] 201
rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 419
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: REAL300025277341 none C[C@@H]1C[C@]2(C(=O)N3CCCC3(C)CNC(=O)CSC3=NNC(=O)[N-]3)C[C@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 9, 9, 9, 19, 37, 37, 37, 96, 126, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 37, 96, 96, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 555
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: REAL300025277341 none C[C@@H]1C[C@]2(C(=O)N3CCCC3(C)CNC(=O)CSC3=NNC(=O)[N-]3)C[C@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 185, 159, 185, 159, 159, 159, 159, 132, 159, 75, 75, 32, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 159, 159, 159, 159, 132, 132, 75, 32, 32, 1, 201, 201] 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])
total number of confs: 755
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277341 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277341
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277341/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277341
Building REAL300025277342
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277342'
/scratch/stefan/7808390/working/building/REAL300025277342 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277342

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277342/0 /scratch/stefan/7808390/working/building/REAL300025277342 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/204
`/scratch/stefan/7808390/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277342 none CNC(=O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 201, 144, 140, 144, 140, 140, 140, 140, 113, 140, 64, 64, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 191, 191, 140, 140, 140, 140, 140, 140, 140, 140, 140, 113, 113, 64, 28, 28, 1] 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])
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: REAL300025277342 none CNC(=O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 24, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 30, 49, 140, 140, 140, 140, 140, 24, 24, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 30, 30, 140] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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
/scratch/stefan/7808390/working/building/REAL300025277342 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277342
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277342/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277342
Building REAL300025277343
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277343'
/scratch/stefan/7808390/working/building/REAL300025277343 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277343

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277343/0 /scratch/stefan/7808390/working/building/REAL300025277343 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/205
`/scratch/stefan/7808390/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1COC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277343 none CC(OC1COC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 23, 23, 23, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 27, 41, 128, 128, 128, 128, 128, 5, 5, 5, 5, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 27, 27, 128] 201
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 312
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277343 none CC(OC1COC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 17, 23, 23, 23, 23, 23, 23, 23, 23, 35, 55, 55, 55, 123, 143, 201, 201, 201, 201, 201, 17, 17, 17, 17, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 35, 35, 55, 123, 123, 201] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 35, 31] set([0, 1, 7, 8, 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, 47, 48, 49, 50])
total number of confs: 679
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: REAL300025277343 none CC(OC1COC1)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [176, 128, 176, 195, 201, 201, 201, 128, 128, 128, 128, 128, 128, 97, 128, 63, 63, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 128, 128, 128, 128, 97, 97, 63, 28, 28, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 832
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277343 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277343
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277343/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277343
Building REAL300025277344
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277344'
/scratch/stefan/7808390/working/building/REAL300025277344 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277344

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277344/0 /scratch/stefan/7808390/working/building/REAL300025277344 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/206
`/scratch/stefan/7808390/working/3D/206' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(F)F)

`REAL300025277344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277344 none CC(=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [181, 181, 108, 106, 108, 106, 106, 106, 106, 89, 106, 53, 53, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 181, 201, 201, 181, 181, 181, 181, 106, 106, 106, 106, 106, 106, 106, 106, 106, 89, 89, 53, 27, 27, 1, 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])
total number of confs: 819
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277344 none CC(=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 37, 41, 106, 106, 106, 106, 106, 10, 41, 41, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 37, 37, 106, 41] 201
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 35, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 381
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277344 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277344
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277344/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277344
Building REAL300025277345
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277345'
/scratch/stefan/7808390/working/building/REAL300025277345 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277345

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277345/0 /scratch/stefan/7808390/working/building/REAL300025277345 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/207
`/scratch/stefan/7808390/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277345 none CCOC(=O)C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 199, 159, 199, 159, 126, 126, 126, 126, 126, 126, 126, 91, 126, 71, 71, 32, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 159, 159, 126, 126, 126, 126, 126, 126, 126, 126, 126, 91, 91, 71, 32, 32, 1] 201
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 777
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277345 none CCOC(=O)C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 4, 10, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 26, 41, 126, 126, 126, 126, 126, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 26, 26, 126] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277345 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277345
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277345/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277345
Building REAL300025277346
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277346'
/scratch/stefan/7808390/working/building/REAL300025277346 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277346

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277346/0 /scratch/stefan/7808390/working/building/REAL300025277346 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/208
`/scratch/stefan/7808390/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277346 none CN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 81, 100, 152, 152, 152, 152, 152, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 21, 81, 81, 152] 163
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 430
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277346 none CN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 21, 55, 55, 55, 124, 139, 163, 163, 163, 163, 163, 2, 2, 2, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 55, 124, 124, 163] 163
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 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])
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: REAL300025277346 none CN1C=NN=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [163, 163, 163, 163, 163, 155, 152, 155, 152, 152, 152, 152, 129, 152, 82, 82, 34, 82, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 152, 152, 152, 152, 152, 152, 152, 152, 152, 129, 129, 82, 34, 34, 1] 163
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])
total number of confs: 601
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277346 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277346
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277346/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277346
Building REAL300025277347
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277347'
/scratch/stefan/7808390/working/building/REAL300025277347 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277347

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277347/0 /scratch/stefan/7808390/working/building/REAL300025277347 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/209
`/scratch/stefan/7808390/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC(N)=N1)

`REAL300025277347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277347 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.pl3', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [152, 127, 66, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 161, 161, 197, 201, 201, 201, 201, 201, 152, 152, 152, 127, 127, 66, 31, 31, 1, 152, 152, 152, 152, 152, 152, 197, 197, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277347 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.pl3', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 5, 11, 11, 11, 39, 59, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 3, 3, 9, 14, 14, 14, 14, 14, 2, 2, 2, 5, 5, 11, 39, 39, 152, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: REAL300025277347 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.pl3', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 14, 14, 26, 45, 45, 45, 107, 133, 201, 201, 201, 201, 201, 14, 14, 14, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 45, 107, 107, 201, 14, 14, 14, 14, 14, 14, 7, 7, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277347 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277347
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277347/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277347
Building REAL300025277348
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277348'
/scratch/stefan/7808390/working/building/REAL300025277348 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277348

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277348/0 /scratch/stefan/7808390/working/building/REAL300025277348 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/210
`/scratch/stefan/7808390/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOCC1)

`REAL300025277348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277348 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 110, 61, 61, 32, 61, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 152, 152, 201, 201, 201, 201, 201, 201, 144, 144, 144, 110, 110, 61, 32, 32, 1, 144, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 707
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277348 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 40, 55, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 12, 40, 40, 144, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 318
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277348 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 37, 37, 37, 110, 131, 201, 201, 201, 201, 201, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 37, 110, 110, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 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/7808390/working/building/REAL300025277348 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277348
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277348/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277348
Building REAL300025277349
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277349'
/scratch/stefan/7808390/working/building/REAL300025277349 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277349

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277349/0 /scratch/stefan/7808390/working/building/REAL300025277349 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/211
`/scratch/stefan/7808390/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277349 none C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 65, 71, 106, 106, 106, 106, 106, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 65, 65, 106] 106
rigid atoms, others: [35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 319
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: REAL300025277349 none C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 7, 19, 19, 19, 65, 71, 106, 106, 106, 106, 106, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 19, 65, 65, 106] 106
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 31] set([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, 46, 47, 48, 49])
total number of confs: 314
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: REAL300025277349 none C[C@@H]1OCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 102, 106, 64, 64, 30, 64, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 102, 102, 64, 30, 30, 1] 106
rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 414
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277349 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277349
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277349/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277349
Building REAL300025277350
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277350'
/scratch/stefan/7808390/working/building/REAL300025277350 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277350

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277350/0 /scratch/stefan/7808390/working/building/REAL300025277350 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/212
`/scratch/stefan/7808390/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(F)C1)

`REAL300025277350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277350 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [102, 82, 61, 61, 29, 61, 12, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 103, 103, 128, 128, 128, 128, 102, 102, 102, 82, 82, 61, 29, 29, 1, 102, 102, 102, 102, 102, 102, 128, 128, 128, 128, 128, 128] 128
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277350 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 51, 59, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 2, 2, 2, 5, 5, 13, 51, 51, 102, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 128
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277350 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [8, 8, 8, 18, 38, 38, 38, 89, 101, 128, 128, 128, 128, 128, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 38, 89, 89, 128, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 128
rigid atoms, others: [40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 414
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277350 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277350
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277350/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277350
Building REAL300025277351
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277351'
/scratch/stefan/7808390/working/building/REAL300025277351 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277351

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277351/0 /scratch/stefan/7808390/working/building/REAL300025277351 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/213
`/scratch/stefan/7808390/working/3D/213' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(O)C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277351 none CCC(O)C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 181, 201, 154, 181, 153, 154, 153, 153, 153, 153, 110, 153, 61, 61, 31, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 181, 181, 181, 181, 153, 153, 153, 153, 153, 153, 153, 153, 153, 110, 110, 61, 31, 31, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1489
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277351 none CCC(O)C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 14, 7, 14, 4, 7, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 38, 55, 153, 153, 153, 153, 153, 16, 16, 16, 16, 16, 14, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 13, 38, 38, 153] 603
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 412
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277351 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277351
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277351/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277351
Building REAL300025277352
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277352'
/scratch/stefan/7808390/working/building/REAL300025277352 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277352

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277352/0 /scratch/stefan/7808390/working/building/REAL300025277352 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/214
`/scratch/stefan/7808390/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)OCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277352 none CCC(C)(C)OCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 152, 201, 201, 127, 120, 118, 120, 118, 118, 118, 118, 90, 118, 57, 57, 28, 57, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 118, 118, 118, 118, 118, 118, 118, 118, 118, 90, 90, 57, 28, 28, 1] 201
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 829
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: REAL300025277352 none CCC(C)(C)OCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 18, 7, 18, 18, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 25, 35, 118, 118, 118, 118, 118, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 25, 25, 118] 201
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 332
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277352 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277352
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277352/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277352
Building REAL300025277353
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277353'
/scratch/stefan/7808390/working/building/REAL300025277353 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277353

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277353/0 /scratch/stefan/7808390/working/building/REAL300025277353 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/215
`/scratch/stefan/7808390/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)N1)

`REAL300025277353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277353 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 89, 44, 44, 26, 44, 12, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 124, 188, 201, 201, 201, 201, 124, 124, 124, 89, 89, 44, 26, 26, 1, 124, 124, 124, 124, 124, 124, 188, 188, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277353 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 30, 36, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 2, 2, 7, 17, 17, 17, 17, 2, 2, 2, 5, 5, 10, 30, 30, 124, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277353 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 36, 63, 63, 63, 117, 128, 201, 201, 201, 201, 201, 17, 17, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 36, 36, 63, 117, 117, 201, 17, 17, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/7808390/working/building/REAL300025277353 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277353
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277353/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277353
Building REAL300025277354
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277354'
/scratch/stefan/7808390/working/building/REAL300025277354 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277354

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277354/0 /scratch/stefan/7808390/working/building/REAL300025277354 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/216
`/scratch/stefan/7808390/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCC1)

`REAL300025277354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277354 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [141, 98, 55, 55, 27, 55, 12, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 153, 153, 183, 183, 201, 201, 201, 141, 141, 141, 98, 98, 55, 27, 27, 1, 141, 141, 141, 141, 141, 141, 183, 549, 201, 201, 201, 201, 201, 201, 201] 603
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 92
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277354 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 5, 9, 9, 9, 30, 42, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 3, 3, 10, 10, 18, 18, 18, 2, 2, 2, 5, 5, 9, 30, 30, 141, 1, 1, 1, 1, 1, 1, 10, 30, 18, 18, 18, 18, 18, 18, 18] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 367
number of broken/clashed sets: 92
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277354 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 57, 57, 57, 115, 134, 201, 201, 201, 201, 201, 18, 18, 18, 17, 6, 17, 1, 6, 1, 1, 1, 1, 18, 18, 18, 34, 34, 57, 115, 115, 201, 18, 18, 18, 18, 18, 18, 6, 18, 1, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 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, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 655
number of broken/clashed sets: 92
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277354 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277354
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277354/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277354
Building REAL300025277355
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277355'
/scratch/stefan/7808390/working/building/REAL300025277355 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277355

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277355/0 /scratch/stefan/7808390/working/building/REAL300025277355 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/217
`/scratch/stefan/7808390/working/3D/217' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCOC(=O)N1)

`REAL300025277355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277355 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCOC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [66, 56, 45, 45, 25, 45, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 68, 68, 85, 85, 85, 85, 85, 85, 66, 66, 66, 56, 56, 45, 25, 25, 1, 66, 66, 66, 66, 66, 66, 85, 85, 85, 85, 85, 85] 85
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277355 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCOC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 38, 41, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 2, 2, 2, 3, 3, 11, 38, 38, 66, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 85
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277355 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCOC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 12, 28, 28, 28, 61, 66, 85, 85, 85, 85, 85, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 28, 61, 61, 85, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 85
rigid atoms, others: [42, 43, 44, 45, 46, 47, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 261
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277355 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277355
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277355/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277355
Building REAL300025277356
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277356'
/scratch/stefan/7808390/working/building/REAL300025277356 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277356

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277356/0 /scratch/stefan/7808390/working/building/REAL300025277356 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/218
`/scratch/stefan/7808390/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+]1CC(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277356 none C[NH+]1CC(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [10, 10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 32, 51, 104, 104, 104, 104, 104, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 32, 32, 104, 10, 10] 107
rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277356 none C[NH+]1CC(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 5, 9, 9, 10, 10, 10, 10, 10, 10, 13, 23, 23, 23, 58, 78, 107, 107, 107, 107, 107, 1, 2, 2, 2, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 23, 58, 58, 107, 1, 1] 107
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 50, 51, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277356 none C[NH+]1CC(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 105, 104, 105, 104, 104, 104, 104, 98, 104, 75, 75, 33, 75, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 104, 104, 104, 104, 104, 104, 104, 104, 104, 98, 98, 75, 33, 33, 1, 107, 107] 107
rigid atoms, others: [49, 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, 50, 51])
total number of confs: 402
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277356 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277356
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277356/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277356
Building REAL300025277357
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277357'
/scratch/stefan/7808390/working/building/REAL300025277357 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277357

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277357/0 /scratch/stefan/7808390/working/building/REAL300025277357 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/219
`/scratch/stefan/7808390/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1)

`REAL300025277357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277357 none CC1=NN=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 58, 80, 177, 177, 177, 177, 177, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 21, 58, 58, 177] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025277357 none CC1=NN=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 9, 9, 9, 24, 59, 59, 59, 121, 141, 201, 201, 201, 201, 201, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 59, 121, 121, 201] 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: 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: REAL300025277357 none CC1=NN=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)S1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 177, 200, 177, 177, 177, 177, 139, 177, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 177, 177, 177, 177, 177, 177, 177, 177, 177, 139, 139, 62, 30, 30, 1] 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])
total number of confs: 776
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277357 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277357
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277357/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277357
Building REAL300025277358
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277358'
/scratch/stefan/7808390/working/building/REAL300025277358 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277358

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277358/0 /scratch/stefan/7808390/working/building/REAL300025277358 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/220
`/scratch/stefan/7808390/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(O)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277358 none CC1(O)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 42, 59, 151, 151, 151, 151, 151, 10, 10, 10, 10, 30, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 12, 42, 42, 151, 10, 10] 603
rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277358 none CC1(O)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 10, 10, 10, 10, 10, 10, 21, 44, 44, 44, 116, 141, 201, 201, 201, 201, 201, 1, 2, 2, 2, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 44, 116, 116, 201, 1, 1] 603
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 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, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277358 none CC1(O)CC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 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, 158, 151, 158, 151, 151, 151, 151, 117, 151, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 201, 201, 201, 151, 151, 151, 151, 151, 151, 151, 151, 151, 117, 117, 62, 30, 30, 1, 201, 201] 603
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])
total number of confs: 1412
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277358 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277358
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277358/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277358
Building REAL300025277359
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277359'
/scratch/stefan/7808390/working/building/REAL300025277359 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277359

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277359/0 /scratch/stefan/7808390/working/building/REAL300025277359 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/221
`/scratch/stefan/7808390/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277359 none CCCCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 179, 120, 179, 112, 120, 112, 112, 112, 112, 75, 112, 50, 50, 28, 50, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 537, 112, 112, 112, 112, 112, 112, 112, 112, 112, 75, 75, 50, 28, 28, 1] 603
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 1409
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: REAL300025277359 none CCCCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 17, 18, 17, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 30, 44, 112, 112, 112, 112, 112, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 30, 30, 112] 603
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 339
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277359 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277359
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277359/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277359
Building REAL300025277360
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277360'
/scratch/stefan/7808390/working/building/REAL300025277360 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277360

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277360/0 /scratch/stefan/7808390/working/building/REAL300025277360 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/222
`/scratch/stefan/7808390/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=N1)

`REAL300025277360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277360 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [137, 104, 59, 59, 29, 59, 12, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 179, 179, 201, 201, 201, 201, 201, 201, 137, 137, 137, 104, 104, 59, 29, 29, 1, 137, 137, 137, 137, 137, 137, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277360 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 11, 11, 11, 39, 55, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 2, 2, 2, 6, 6, 11, 39, 39, 137, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
total number of confs: 310
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277360 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 45, 45, 45, 116, 136, 201, 201, 201, 201, 201, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 24, 24, 45, 116, 116, 201, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277360 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277360
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277360/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277360
Building REAL300025277361
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277361'
/scratch/stefan/7808390/working/building/REAL300025277361 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277361

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277361/0 /scratch/stefan/7808390/working/building/REAL300025277361 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/223
`/scratch/stefan/7808390/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(O)C=C1)

`REAL300025277361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277361 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [190, 153, 86, 86, 33, 86, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 153, 153, 86, 33, 33, 1, 190, 190, 190, 190, 190, 190, 201, 201, 402, 201, 201] 402
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1179
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: REAL300025277361 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 6, 17, 17, 17, 56, 88, 190, 190, 190, 190, 190, 1, 1, 1, 1, 1, 4, 4, 9, 9, 4, 7, 9, 9, 2, 2, 2, 6, 6, 17, 56, 56, 190, 1, 1, 1, 1, 1, 1, 9, 9, 18, 9, 9] 402
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
total number of confs: 477
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277361 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 19, 41, 41, 41, 114, 143, 201, 201, 201, 201, 201, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 41, 114, 114, 201, 9, 9, 9, 9, 9, 9, 1, 1, 2, 1, 1] 402
rigid atoms, others: [42, 43, 45, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 592
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277361 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277361
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277361/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277361
Building REAL300025277362
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277362'
/scratch/stefan/7808390/working/building/REAL300025277362 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277362

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277362/0 /scratch/stefan/7808390/working/building/REAL300025277362 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/224
`/scratch/stefan/7808390/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277362 none C=CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 129, 129, 129, 129, 129, 129, 129, 106, 129, 65, 65, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 129, 129, 129, 129, 106, 106, 65, 27, 27, 1] 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])
total number of confs: 864
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277362 none C=CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 43, 46, 129, 129, 129, 129, 129, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 10, 43, 43, 129] 201
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277362 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277362
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277362/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277362
Building REAL300025277363
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277363'
/scratch/stefan/7808390/working/building/REAL300025277363 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277363

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277363/0 /scratch/stefan/7808390/working/building/REAL300025277363 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/225
`/scratch/stefan/7808390/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277363 none C[NH+](C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 18, 19, 18, 18, 18, 18, 18, 18, 15, 15, 10, 15, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 10, 10, 1] 19
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])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277363 none C[NH+](C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 14, 14, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 14, 14, 18] 19
rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277363 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277363/1 /scratch/stefan/7808390/working/building/REAL300025277363 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/226
`/scratch/stefan/7808390/working/3D/226' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277363.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277363/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277363 none CN(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 59, 59, 59, 59, 59, 59, 59, 47, 59, 27, 27, 16, 27, 11, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 59, 59, 59, 59, 59, 59, 59, 59, 59, 47, 47, 27, 16, 16, 1] 82
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])
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: REAL300025277363 none CN(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [18, 10, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 30, 30, 59, 59, 59, 59, 59, 18, 18, 18, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 30, 30, 59] 82
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277363 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277363
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277363/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277363/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277363
Building REAL300025277364
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277364'
/scratch/stefan/7808390/working/building/REAL300025277364 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277364

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277364/0 /scratch/stefan/7808390/working/building/REAL300025277364 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/227
`/scratch/stefan/7808390/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=C1)

`REAL300025277364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277364 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [119, 87, 53, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 125, 125, 201, 201, 201, 201, 201, 201, 119, 119, 119, 87, 87, 53, 30, 30, 1, 119, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 647
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277364 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 11, 11, 11, 34, 49, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 11, 34, 34, 119, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 266
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: REAL300025277364 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 21, 40, 40, 40, 102, 125, 201, 201, 201, 201, 201, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 40, 102, 102, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 1] 201
rigid atoms, others: [42, 43, 44, 47, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46])
total number of confs: 587
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277364 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277364
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277364/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277364
Building REAL300025277365
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277365'
/scratch/stefan/7808390/working/building/REAL300025277365 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277365

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277365/0 /scratch/stefan/7808390/working/building/REAL300025277365 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/228
`/scratch/stefan/7808390/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC#N)

`REAL300025277365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277365 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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: [75, 68, 49, 49, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 83, 83, 75, 75, 75, 68, 68, 49, 25, 25, 1, 75, 75, 75, 75, 75, 75, 83, 83] 83
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: REAL300025277365 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 10, 10, 10, 39, 44, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 3, 3, 9, 9, 2, 2, 2, 3, 3, 10, 39, 39, 75, 1, 1, 1, 1, 1, 1, 9, 9] 83
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 14, 15, 16, 17, 18, 37] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277365 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277365
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277365/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277365
Building REAL300025277366
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277366'
/scratch/stefan/7808390/working/building/REAL300025277366 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277366

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277366/0 /scratch/stefan/7808390/working/building/REAL300025277366 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/229
`/scratch/stefan/7808390/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1)

`REAL300025277366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277366 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [189, 150, 84, 84, 33, 84, 13, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 150, 150, 84, 33, 33, 1, 189, 189, 189, 189, 189, 189, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 780
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277366 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 6, 15, 15, 15, 57, 91, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 4, 4, 7, 7, 4, 5, 7, 7, 2, 2, 2, 6, 6, 15, 57, 57, 189, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 459
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: REAL300025277366 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [7, 7, 7, 19, 41, 41, 41, 108, 139, 201, 201, 201, 201, 201, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 41, 108, 108, 201, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 1, 1] 201
rigid atoms, others: [42, 43, 46, 47, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45])
total number of confs: 606
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277366 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277366
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277366/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277366
Building REAL300025277367
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277367'
/scratch/stefan/7808390/working/building/REAL300025277367 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277367

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277367/0 /scratch/stefan/7808390/working/building/REAL300025277367 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/230
`/scratch/stefan/7808390/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1F)

`REAL300025277367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277367 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 118, 70, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 164, 164, 201, 201, 201, 201, 201, 201, 151, 151, 151, 118, 118, 70, 31, 31, 1, 151, 151, 151, 151, 151, 151, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 717
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277367 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 41, 61, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 2, 5, 5, 10, 41, 41, 151, 1, 1, 1, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 332
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277367 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 40, 40, 103, 131, 201, 201, 201, 201, 201, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 40, 103, 103, 201, 11, 11, 11, 11, 11, 11, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 587
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277367 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277367
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277367/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277367
Building REAL300025277368
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277368'
/scratch/stefan/7808390/working/building/REAL300025277368 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277368

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277368/0 /scratch/stefan/7808390/working/building/REAL300025277368 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/231
`/scratch/stefan/7808390/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1C(C)C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277368 none CCOC1C(C)C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 34, 50, 131, 131, 131, 131, 131, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 34, 34, 131] 201
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277368 none CCOC1C(C)C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 14, 25, 25, 25, 71, 97, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 25, 71, 71, 201] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 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, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277368 none CCOC1C(C)C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 131, 136, 131, 131, 131, 131, 95, 131, 58, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 131, 131, 131, 131, 95, 95, 58, 28, 28, 1] 201
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 751
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277368 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277368
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277368/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277368
Building REAL300025277369
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277369'
/scratch/stefan/7808390/working/building/REAL300025277369 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277369

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277369/0 /scratch/stefan/7808390/working/building/REAL300025277369 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/232
`/scratch/stefan/7808390/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC1F)

`REAL300025277369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277369 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [151, 122, 84, 84, 35, 84, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 152, 152, 184, 184, 184, 151, 151, 151, 122, 122, 84, 35, 35, 1, 151, 151, 151, 151, 151, 151, 184, 184, 184, 184] 184
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 699
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277369 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 62, 75, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 2, 2, 2, 5, 5, 15, 62, 62, 151, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 184
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42])
total number of confs: 381
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277369 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 20, 52, 52, 52, 128, 146, 184, 184, 184, 184, 184, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 8, 8, 8, 20, 20, 52, 128, 128, 184, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 184
rigid atoms, others: [39, 40, 41, 42, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 603
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277369 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277369
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277369/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277369
Building REAL300025277370
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277370'
/scratch/stefan/7808390/working/building/REAL300025277370 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277370

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277370/0 /scratch/stefan/7808390/working/building/REAL300025277370 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/233
`/scratch/stefan/7808390/working/3D/233' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(OCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CCC1)

`REAL300025277370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277370 none CC1(OCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 29, 45, 134, 134, 134, 134, 134, 24, 24, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 29, 29, 134, 24, 24, 24, 24, 24, 24] 201
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277370 none CC1(OCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 12, 22, 22, 24, 24, 24, 24, 24, 24, 34, 51, 51, 51, 112, 139, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 34, 34, 51, 112, 112, 201, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([3, 4, 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])
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: REAL300025277370 none CC1(OCC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 172, 167, 139, 134, 139, 134, 134, 134, 134, 98, 134, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 167, 167, 134, 134, 134, 134, 134, 134, 134, 134, 134, 98, 98, 68, 28, 28, 1, 201, 201, 201, 201, 201, 201] 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, 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/7808390/working/building/REAL300025277370 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277370
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277370/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277370
Building REAL300025277371
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277371'
/scratch/stefan/7808390/working/building/REAL300025277371 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277371

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277371/0 /scratch/stefan/7808390/working/building/REAL300025277371 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/234
`/scratch/stefan/7808390/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C)

`REAL300025277371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277371 none C[C@@H](C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 25, 26, 23, 23, 15, 23, 10, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 23, 15, 15, 1, 26, 26, 26, 26, 26, 26] 26
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: 80
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277371 none C[C@@H](C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 16, 17, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 16, 16, 26, 4, 4, 4, 4, 4, 4] 26
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 35, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 91
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277371 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277371/1 /scratch/stefan/7808390/working/building/REAL300025277371 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/235
`/scratch/stefan/7808390/working/3D/235' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N(C)C)

`REAL300025277371.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277371/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277371 none C[C@@H](C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 111, 114, 111, 111, 111, 111, 111, 111, 91, 111, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 111, 111, 111, 111, 111, 111, 111, 111, 111, 91, 91, 61, 29, 29, 1, 114, 114, 114, 114, 114, 114] 114
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: 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: REAL300025277371 none C[C@@H](C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 51, 60, 111, 111, 111, 111, 111, 5, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 51, 51, 111, 9, 9, 9, 9, 9, 9] 114
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 4, 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, 46, 47, 48, 49])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277371 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277371
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277371/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277371/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277371
Building REAL300025277372
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277372'
/scratch/stefan/7808390/working/building/REAL300025277372 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277372

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277372/0 /scratch/stefan/7808390/working/building/REAL300025277372 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/236
`/scratch/stefan/7808390/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)N=C1)

`REAL300025277372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277372 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [183, 129, 67, 67, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 129, 129, 67, 31, 31, 1, 183, 183, 183, 183, 183, 183, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277372 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 20, 20, 20, 62, 85, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 4, 4, 9, 9, 4, 4, 9, 9, 2, 2, 2, 7, 7, 20, 62, 62, 183, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 458
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: REAL300025277372 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 43, 43, 43, 101, 124, 201, 201, 201, 201, 201, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 43, 101, 101, 201, 8, 8, 8, 8, 8, 8, 1, 2, 2, 1] 201
rigid atoms, others: [42, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 570
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277372 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277372
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277372/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277372
Building REAL300025277373
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277373'
/scratch/stefan/7808390/working/building/REAL300025277373 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277373

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277373/0 /scratch/stefan/7808390/working/building/REAL300025277373 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/237
`/scratch/stefan/7808390/working/3D/237' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCF)

`REAL300025277373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277373 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [159, 133, 86, 86, 33, 86, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 159, 190, 190, 159, 159, 159, 133, 133, 86, 33, 33, 1, 159, 159, 159, 159, 159, 159, 190, 190, 190, 190] 190
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 771
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277373 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 16, 16, 16, 65, 79, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 2, 2, 8, 12, 2, 2, 2, 5, 5, 16, 65, 65, 159, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12] 190
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 14, 15, 16, 17, 18, 37] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41])
total number of confs: 425
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277373 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277373
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277373/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277373
Building REAL300025277374
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277374'
/scratch/stefan/7808390/working/building/REAL300025277374 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277374

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277374/0 /scratch/stefan/7808390/working/building/REAL300025277374 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/238
`/scratch/stefan/7808390/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(F)=NN1)

`REAL300025277374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277374 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(F)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [76, 64, 42, 42, 24, 42, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 78, 78, 87, 87, 87, 87, 87, 76, 76, 76, 64, 64, 42, 24, 24, 1, 76, 76, 76, 76, 76, 76, 87, 87] 87
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 305
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277374 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(F)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 6, 13, 13, 13, 39, 44, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 2, 2, 2, 6, 6, 13, 39, 39, 76, 1, 1, 1, 1, 1, 1, 13, 13] 87
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 225
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277374 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(F)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 23, 44, 44, 44, 72, 75, 87, 87, 87, 87, 87, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 44, 72, 72, 87, 13, 13, 13, 13, 13, 13, 1, 1] 87
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 296
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277374 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277374
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277374/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277374
Building REAL300025277375
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277375'
/scratch/stefan/7808390/working/building/REAL300025277375 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277375

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277375/0 /scratch/stefan/7808390/working/building/REAL300025277375 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/239
`/scratch/stefan/7808390/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C=CCC1)

`REAL300025277375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277375 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [101, 86, 62, 62, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 102, 102, 118, 118, 118, 118, 101, 101, 101, 86, 86, 62, 31, 31, 1, 101, 101, 101, 101, 101, 101, 118, 118, 118, 118, 118, 118, 118] 118
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277375 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 50, 59, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 2, 2, 2, 5, 5, 13, 50, 50, 101, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 118
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277375 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 15, 32, 32, 32, 77, 90, 118, 118, 118, 118, 118, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 32, 77, 77, 118, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 118
rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 363
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277375 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277375
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277375/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277375
Building REAL300025277376
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277376'
/scratch/stefan/7808390/working/building/REAL300025277376 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277376

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277376/0 /scratch/stefan/7808390/working/building/REAL300025277376 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/240
`/scratch/stefan/7808390/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC(O)C1)

`REAL300025277376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277376 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [135, 95, 55, 55, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 146, 146, 201, 201, 201, 201, 201, 201, 135, 135, 135, 95, 95, 55, 27, 27, 1, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1391
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277376 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 6, 15, 15, 15, 43, 62, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 2, 6, 6, 15, 43, 43, 135, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 33, 11, 11] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277376 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [11, 11, 11, 24, 42, 42, 42, 97, 121, 201, 201, 201, 201, 201, 11, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 24, 42, 97, 97, 201, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1] 603
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 50])
total number of confs: 562
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277376 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277376
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277376/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277376
Building REAL300025277377
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277377'
/scratch/stefan/7808390/working/building/REAL300025277377 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277377

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277377/0 /scratch/stefan/7808390/working/building/REAL300025277377 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/241
`/scratch/stefan/7808390/working/3D/241' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1CCOC1)

`REAL300025277377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277377 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [129, 95, 55, 55, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 131, 131, 196, 196, 201, 201, 201, 201, 129, 129, 129, 95, 95, 55, 28, 28, 1, 129, 129, 129, 129, 129, 129, 196, 196, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277377 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 4, 8, 8, 8, 30, 43, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 3, 3, 10, 10, 23, 23, 23, 23, 2, 2, 2, 4, 4, 8, 30, 30, 129, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 23, 23] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277377 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [23, 23, 23, 37, 59, 59, 59, 120, 140, 201, 201, 201, 201, 201, 23, 23, 23, 22, 6, 22, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 37, 37, 59, 120, 120, 201, 23, 23, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/7808390/working/building/REAL300025277377 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277377
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277377/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277377
Building REAL300025277378
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277378'
/scratch/stefan/7808390/working/building/REAL300025277378 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277378

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277378/0 /scratch/stefan/7808390/working/building/REAL300025277378 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/242
`/scratch/stefan/7808390/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277378 none COC(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 182, 152, 199, 149, 152, 149, 149, 149, 149, 122, 149, 83, 83, 32, 83, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 597, 149, 149, 149, 149, 149, 149, 149, 149, 149, 122, 122, 83, 32, 32, 1] 603
rigid atoms, others: [49, 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])
total number of confs: 1571
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: REAL300025277378 none COC(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 14, 8, 13, 3, 8, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 40, 67, 149, 149, 149, 149, 149, 16, 16, 16, 14, 14, 14, 14, 8, 24, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 40, 40, 149] 603
rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 415
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277378 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277378
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277378/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277378
Building REAL300025277379
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277379'
/scratch/stefan/7808390/working/building/REAL300025277379 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277379

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277379/0 /scratch/stefan/7808390/working/building/REAL300025277379 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/243
`/scratch/stefan/7808390/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CNC(=O)N1)

`REAL300025277379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277379 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CNC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [65, 60, 42, 42, 21, 42, 11, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 66, 66, 74, 74, 74, 74, 74, 74, 65, 65, 65, 60, 60, 42, 21, 21, 1, 65, 65, 65, 65, 65, 65, 74, 74, 74, 74] 74
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277379 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CNC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 11, 11, 11, 36, 40, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 2, 2, 2, 3, 3, 11, 36, 36, 65, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 74
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 199
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277379 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CNC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 10, 26, 26, 26, 53, 58, 74, 74, 74, 74, 74, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 26, 53, 53, 74, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 74
rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 242
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277379 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277379
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277379/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277379
Building REAL300025277380
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277380'
/scratch/stefan/7808390/working/building/REAL300025277380 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277380

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277380/0 /scratch/stefan/7808390/working/building/REAL300025277380 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/244
`/scratch/stefan/7808390/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277380 none CCSC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 147, 180, 144, 147, 144, 144, 144, 144, 104, 144, 55, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 180, 180, 144, 144, 144, 144, 144, 144, 144, 144, 144, 104, 104, 55, 30, 30, 1] 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])
total number of confs: 803
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277380 none CCSC(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 43, 59, 144, 144, 144, 144, 144, 15, 15, 15, 15, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 13, 43, 43, 144] 201
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277380 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277380
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277380/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277380
Building REAL300025277381
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277381'
/scratch/stefan/7808390/working/building/REAL300025277381 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277381

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277381/0 /scratch/stefan/7808390/working/building/REAL300025277381 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/245
`/scratch/stefan/7808390/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CC(C)C1)

`REAL300025277381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277381 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CC(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.4', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
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, 4, 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, 5, 5, 5] 5
rigid atoms, others: [46, 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, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 11
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277381 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CC(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.4', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
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, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 4, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 5, 2, 2, 2, 2, 2, 2, 2, 2] 5
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 36, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277381 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CC(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.4', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5, 1, 1, 1, 2, 2, 2, 1, 1] 5
rigid atoms, others: [1, 54, 47, 48, 49, 53, 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, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52])
total number of confs: 23
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277381 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277381/1 /scratch/stefan/7808390/working/building/REAL300025277381 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/246
`/scratch/stefan/7808390/working/3D/246' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CC(C)C1)

`REAL300025277381.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277381/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277381 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CC(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 181, 164, 181, 164, 164, 164, 164, 119, 164, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 164, 164, 164, 164, 119, 119, 66, 29, 29, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [45, 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, 44, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 845
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277381 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CC(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 39, 58, 164, 164, 164, 164, 164, 9, 11, 11, 11, 11, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 39, 39, 164, 11, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 36, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277381 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CC(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 9, 11, 11, 11, 11, 11, 11, 25, 40, 40, 40, 99, 125, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 40, 99, 99, 201, 1, 1, 1, 2, 2, 2, 1, 1] 201
rigid atoms, others: [1, 46, 47, 48, 52, 53, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51])
total number of confs: 595
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277381 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277381
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277381/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277381/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277381
Building REAL300025277382
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277382'
/scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277382

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277382/0 /scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/247
`/scratch/stefan/7808390/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[N@@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277382 none CC1CC[N@@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 6, 7, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 6, 6, 15] 15
rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277382 none CC1CC[N@@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 7, 8, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 15] 15
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 5, 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, 46, 47, 48, 49, 50, 51])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277382 none CC1CC[N@@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 1] 15
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 43
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277382/1 /scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/248
`/scratch/stefan/7808390/working/3D/248' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[N@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277382.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277382/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277382 none CC1CC[N@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 10, 12, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 10, 10, 20] 20
rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277382 none CC1CC[N@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 12, 14, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 12, 20] 20
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 5, 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, 46, 47, 48, 49, 50, 51])
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: REAL300025277382 none CC1CC[N@H+]1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 20, 17, 17, 16, 17, 11, 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, 20, 18, 18, 17, 16, 16, 1] 20
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 57
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277382/2 /scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/249
`/scratch/stefan/7808390/working/3D/249' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277382.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277382/2/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: REAL300025277382 none CC1CCN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 45, 74, 159, 159, 159, 159, 159, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 45, 45, 159] 201
rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277382 none CC1CCN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 15, 15, 15, 15, 15, 15, 27, 46, 46, 46, 105, 138, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 46, 105, 105, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 29, 30, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277382 none CC1CCN1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 159, 186, 159, 159, 159, 159, 130, 159, 80, 80, 33, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 159, 159, 159, 159, 130, 130, 80, 33, 33, 1] 201
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])
total number of confs: 794
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277382 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277382
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277382/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277382/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277382/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277382
Building REAL300025277383
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277383'
/scratch/stefan/7808390/working/building/REAL300025277383 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277383

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277383/0 /scratch/stefan/7808390/working/building/REAL300025277383 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/250
`/scratch/stefan/7808390/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277383 none C[NH+](C)CC=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 63, 63, 50, 50, 50, 50, 50, 50, 50, 47, 50, 35, 35, 26, 35, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 63, 63, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 35, 26, 26, 1] 68
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277383 none C[NH+](C)CC=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 18, 22, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 18, 18, 50] 68
rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277383 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277383
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277383/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277383
Building REAL300025277384
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277384'
/scratch/stefan/7808390/working/building/REAL300025277384 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277384

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277384/0 /scratch/stefan/7808390/working/building/REAL300025277384 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/251
`/scratch/stefan/7808390/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCSC1)

`REAL300025277384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277384 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [83, 73, 57, 57, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 115, 115, 115, 115, 83, 83, 83, 73, 73, 57, 30, 30, 1, 83, 83, 83, 83, 83, 83, 115, 115, 115, 115, 115] 115
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 372
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277384 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 39, 47, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 2, 2, 2, 5, 5, 13, 39, 39, 83, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 115
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44])
total number of confs: 232
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: REAL300025277384 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 16, 36, 36, 36, 82, 92, 115, 115, 115, 115, 115, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 36, 82, 82, 115, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 115
rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 388
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277384 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277384
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277384/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277384
Building REAL300025277385
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277385'
/scratch/stefan/7808390/working/building/REAL300025277385 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277385

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277385/0 /scratch/stefan/7808390/working/building/REAL300025277385 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/252
`/scratch/stefan/7808390/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC(F)F)

`REAL300025277385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277385 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 71, 50, 50, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 181, 199, 201, 201, 201, 108, 108, 108, 71, 71, 50, 28, 28, 1, 108, 108, 108, 108, 108, 108, 181, 181, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277385 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 5, 5, 5, 20, 30, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 2, 2, 6, 8, 9, 18, 18, 2, 2, 2, 3, 3, 5, 20, 20, 108, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 18] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 278
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277385 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277385
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277385/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277385
Building REAL300025277386
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277386'
/scratch/stefan/7808390/working/building/REAL300025277386 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277386

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277386/0 /scratch/stefan/7808390/working/building/REAL300025277386 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/253
`/scratch/stefan/7808390/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CN(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277386 none CC1(C)CN(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 34, 52, 139, 139, 139, 139, 139, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 34, 34, 139, 19, 19] 201
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277386 none CC1(C)CN(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 16, 16, 19, 19, 19, 19, 19, 19, 33, 52, 52, 52, 107, 128, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 52, 107, 107, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 52, 53, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277386 none CC1(C)CN(CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 139, 150, 139, 139, 139, 139, 99, 139, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 139, 139, 139, 139, 99, 99, 62, 29, 29, 1, 201, 201] 201
rigid atoms, others: [51, 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, 50, 52, 53])
total number of confs: 846
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277386 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277386/1 /scratch/stefan/7808390/working/building/REAL300025277386 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/254
`/scratch/stefan/7808390/working/3D/254' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C[NH+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277386.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277386/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277386 none CC1(C)C[NH+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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, 4, 4, 4, 3, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 9, 13, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 9, 9, 21, 4, 4] 28
rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277386 none CC1(C)C[NH+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 13, 18, 28, 28, 28, 28, 28, 1, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 13, 13, 28, 1, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 53, 54, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277386 none CC1(C)C[NH+](CC(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 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]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 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, 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, 21, 28, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 17, 16, 17, 10, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 16, 16, 1, 28, 28] 28
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54])
total number of confs: 100
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277386 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277386
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277386/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277386/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277386
Building REAL300025277387
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277387'
/scratch/stefan/7808390/working/building/REAL300025277387 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277387

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277387/0 /scratch/stefan/7808390/working/building/REAL300025277387 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/255
`/scratch/stefan/7808390/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277387 none CO[C@H](C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 26, 28, 28, 26, 26, 26, 26, 26, 26, 24, 26, 18, 18, 12, 18, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 24, 18, 12, 12, 1] 28
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])
total number of confs: 114
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277387 none CO[C@H](C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [8, 5, 2, 5, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 18, 18, 26, 26, 26, 26, 26, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 18, 18, 26] 28
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 108
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277387 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277387
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277387/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277387
Building REAL300025277388
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277388'
/scratch/stefan/7808390/working/building/REAL300025277388 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277388

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277388/0 /scratch/stefan/7808390/working/building/REAL300025277388 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/256
`/scratch/stefan/7808390/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C12CCC(C1)OC2)

`REAL300025277388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277388 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C12CCC(C1)OC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [138, 115, 74, 74, 32, 74, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 153, 153, 167, 167, 167, 167, 167, 167, 138, 138, 138, 115, 115, 74, 32, 32, 1, 138, 138, 138, 138, 138, 138, 167, 167, 167, 167, 167, 167, 167, 167, 167] 167
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 620
number of broken/clashed sets: 88
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277388 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C12CCC(C1)OC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 5, 17, 17, 17, 61, 70, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 17, 61, 61, 138, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 167
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 361
number of broken/clashed sets: 88
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277388 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C12CCC(C1)OC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 19, 42, 42, 42, 115, 126, 167, 167, 167, 167, 167, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 42, 115, 115, 167, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 167
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 546
number of broken/clashed sets: 88
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277388 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277388
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277388/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277388
Building REAL300025277389
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277389'
/scratch/stefan/7808390/working/building/REAL300025277389 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277389

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277389/0 /scratch/stefan/7808390/working/building/REAL300025277389 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/257
`/scratch/stefan/7808390/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC12CC(O)C2)

`REAL300025277389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277389 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC12CC(O)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [135, 106, 59, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 143, 143, 201, 201, 201, 201, 201, 201, 135, 135, 135, 106, 106, 59, 30, 30, 1, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 1362
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277389 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC12CC(O)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 5, 10, 10, 10, 36, 50, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 10, 36, 36, 135, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 27, 9, 9] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277389 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC12CC(O)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [9, 9, 9, 23, 44, 44, 44, 105, 126, 201, 201, 201, 201, 201, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 44, 105, 105, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 6, 1, 1] 603
rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48])
total number of confs: 599
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277389 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277389
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277389/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277389
Building REAL300025277390
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277390'
/scratch/stefan/7808390/working/building/REAL300025277390 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277390

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277390/0 /scratch/stefan/7808390/working/building/REAL300025277390 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/258
`/scratch/stefan/7808390/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NNC=C1)

`REAL300025277390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277390 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [163, 123, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 170, 170, 196, 196, 201, 201, 201, 201, 163, 163, 163, 123, 123, 69, 30, 30, 1, 163, 163, 163, 163, 163, 163, 196, 196, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277390 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 6, 12, 12, 12, 40, 64, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 3, 3, 9, 9, 16, 16, 16, 16, 2, 2, 2, 6, 6, 12, 40, 40, 163, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277390 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=NNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [16, 16, 16, 32, 52, 52, 52, 118, 142, 201, 201, 201, 201, 201, 16, 16, 16, 14, 6, 14, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 32, 32, 52, 118, 118, 201, 16, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/7808390/working/building/REAL300025277390 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277390
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277390/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277390
Building REAL300025277391
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277391'
/scratch/stefan/7808390/working/building/REAL300025277391 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277391

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277391/0 /scratch/stefan/7808390/working/building/REAL300025277391 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/259
`/scratch/stefan/7808390/working/3D/259' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(F)F)

`REAL300025277391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277391 none CC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 100, 100, 100, 100, 100, 100, 100, 85, 100, 51, 51, 25, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 189, 189, 100, 100, 100, 100, 100, 100, 100, 100, 100, 85, 85, 51, 25, 25, 1, 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])
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: REAL300025277391 none CC(CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 39, 40, 100, 100, 100, 100, 100, 21, 31, 31, 21, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 39, 39, 100, 31] 201
rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 37] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277391 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277391
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277391/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277391
Building REAL300025277392
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277392'
/scratch/stefan/7808390/working/building/REAL300025277392 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277392

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277392/0 /scratch/stefan/7808390/working/building/REAL300025277392 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/260
`/scratch/stefan/7808390/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CCC[C@H]1O)

`REAL300025277392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277392 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CCC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [105, 76, 53, 53, 28, 53, 12, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 111, 111, 194, 201, 201, 201, 201, 201, 201, 201, 105, 105, 105, 76, 76, 53, 28, 28, 1, 105, 105, 105, 105, 105, 105, 194, 194, 201, 201, 201, 201, 201, 201, 603] 603
rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1457
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277392 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CCC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 4, 8, 8, 8, 26, 41, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 3, 3, 10, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 4, 4, 8, 26, 26, 105, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16, 16, 48] 603
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 326
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277392 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[C@@H]1CCC[C@H]1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 28, 49, 49, 49, 105, 121, 201, 201, 201, 201, 201, 16, 16, 16, 14, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 28, 28, 49, 105, 105, 201, 16, 16, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 3] 603
rigid atoms, others: [46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52])
total number of confs: 622
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277392 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277392
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277392/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277392
Building REAL300025277393
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277393'
/scratch/stefan/7808390/working/building/REAL300025277393 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277393

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277393/0 /scratch/stefan/7808390/working/building/REAL300025277393 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/261
`/scratch/stefan/7808390/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(=O)C=C1)

`REAL300025277393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277393 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 111, 60, 60, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 159, 159, 201, 201, 201, 201, 201, 201, 150, 150, 150, 111, 111, 60, 31, 31, 1, 150, 150, 150, 150, 150, 150, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 734
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277393 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 44, 59, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 2, 2, 2, 5, 5, 13, 44, 44, 150, 1, 1, 1, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 340
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: REAL300025277393 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COC(=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 49, 49, 113, 128, 201, 201, 201, 201, 201, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 49, 113, 113, 201, 10, 10, 10, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 612
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277393 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277393
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277393/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277393
Building REAL300025277394
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277394'
/scratch/stefan/7808390/working/building/REAL300025277394 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277394

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277394/0 /scratch/stefan/7808390/working/building/REAL300025277394 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/262
`/scratch/stefan/7808390/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277394 none CCOC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 192, 108, 192, 76, 33, 33, 33, 33, 33, 33, 33, 20, 33, 16, 16, 12, 16, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 108, 108, 76, 76, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 16, 12, 12, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 785
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277394 none CCOC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 51, 15, 51, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 13, 15, 33, 33, 33, 33, 33, 81, 81, 81, 81, 81, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 13, 13, 33] 201
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 401
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277394 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277394
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277394/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277394
Building REAL300025277395
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277395'
/scratch/stefan/7808390/working/building/REAL300025277395 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277395

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277395/0 /scratch/stefan/7808390/working/building/REAL300025277395 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/263
`/scratch/stefan/7808390/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277395 none CC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 185, 118, 118, 118, 118, 118, 118, 118, 89, 118, 63, 63, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 185, 185, 118, 118, 118, 118, 118, 118, 118, 118, 118, 89, 89, 63, 28, 28, 1] 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])
total number of confs: 894
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277395 none CC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 25, 38, 118, 118, 118, 118, 118, 26, 26, 26, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 25, 25, 118] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277395 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277395
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277395/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277395
Building REAL300025277396
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277396'
/scratch/stefan/7808390/working/building/REAL300025277396 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277396

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277396/0 /scratch/stefan/7808390/working/building/REAL300025277396 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/264
`/scratch/stefan/7808390/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCCC1)

`REAL300025277396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277396 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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: [168, 123, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 181, 181, 201, 201, 201, 201, 201, 201, 168, 168, 168, 123, 123, 62, 30, 30, 1, 168, 168, 168, 168, 168, 168, 201, 201, 603, 201, 201, 201, 201, 201, 201, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1425
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277396 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 6, 16, 16, 16, 42, 61, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 4, 4, 11, 15, 15, 15, 15, 15, 2, 2, 2, 6, 6, 16, 42, 42, 168, 1, 1, 1, 1, 1, 1, 11, 11, 45, 15, 15, 15, 15, 15, 15, 15, 15] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277396 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 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, 29, 50, 50, 50, 109, 136, 201, 201, 201, 201, 201, 15, 15, 15, 11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 50, 109, 109, 201, 15, 15, 15, 15, 15, 15, 4, 4, 6, 1, 1, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277396 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277396
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277396/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277396
Building REAL300025277397
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277397'
/scratch/stefan/7808390/working/building/REAL300025277397 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277397

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277397/0 /scratch/stefan/7808390/working/building/REAL300025277397 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/265
`/scratch/stefan/7808390/working/3D/265' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC1O)

`REAL300025277397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277397 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
288  conformations in input
total number of sets (complete confs): 288
using faster count positions algorithm for large data
unique positions, atoms: [82, 75, 53, 53, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 96, 96, 96, 96, 96, 82, 82, 82, 75, 75, 53, 27, 27, 1, 82, 82, 82, 82, 82, 82, 96, 96, 96, 96, 96, 96, 96, 96, 288] 288
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 647
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: REAL300025277397 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
288  conformations in input
total number of sets (complete confs): 288
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 16, 16, 16, 42, 50, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 16, 42, 42, 82, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18] 288
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 256
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: REAL300025277397 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
288  conformations in input
total number of sets (complete confs): 288
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 14, 35, 35, 35, 78, 86, 96, 96, 96, 96, 96, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 35, 78, 78, 96, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3] 288
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49])
total number of confs: 340
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277397 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277397
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277397/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277397
Building REAL300025277398
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277398'
/scratch/stefan/7808390/working/building/REAL300025277398 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277398

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277398/0 /scratch/stefan/7808390/working/building/REAL300025277398 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/266
`/scratch/stefan/7808390/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277398 none C[C@@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens need rotated
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [129, 123, 129, 129, 121, 123, 121, 121, 121, 121, 114, 121, 82, 82, 33, 82, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 387, 121, 121, 121, 121, 121, 121, 121, 121, 121, 114, 114, 82, 33, 33, 1] 387
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])
total number of confs: 885
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: REAL300025277398 none C[C@@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens need rotated
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 7, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 58, 79, 121, 121, 121, 121, 121, 7, 7, 7, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 58, 58, 121] 387
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 368
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277398 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277398
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277398/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277398
Building REAL300025277399
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277399'
/scratch/stefan/7808390/working/building/REAL300025277399 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277399

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277399/0 /scratch/stefan/7808390/working/building/REAL300025277399 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/267
`/scratch/stefan/7808390/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[NH+](CC)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277399 none CC[NH+](CC)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 54, 59, 59, 59, 50, 49, 50, 49, 49, 49, 49, 45, 49, 35, 35, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 54, 54, 49, 49, 49, 49, 49, 49, 49, 49, 49, 45, 45, 35, 25, 25, 1] 59
rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 243
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277399 none CC[NH+](CC)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [13, 12, 8, 12, 12, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 19, 22, 49, 49, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 8, 19, 19, 49] 59
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 7, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 184
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277399 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277399
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277399/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277399
Building REAL300025277400
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277400'
/scratch/stefan/7808390/working/building/REAL300025277400 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277400

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277400/0 /scratch/stefan/7808390/working/building/REAL300025277400 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/268
`/scratch/stefan/7808390/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1)

`REAL300025277400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277400 none CC1=CC=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 38, 55, 146, 146, 146, 146, 146, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 38, 38, 146, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277400 none CC1=CC=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 12, 12, 12, 12, 12, 12, 24, 41, 41, 41, 112, 141, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 41, 112, 112, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 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: 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: REAL300025277400 none CC1=CC=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 176, 146, 176, 146, 146, 146, 146, 109, 146, 60, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 146, 146, 146, 146, 146, 146, 146, 146, 146, 109, 109, 60, 28, 28, 1, 201] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/7808390/working/building/REAL300025277400 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277400
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277400/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277400
Building REAL300025277401
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277401'
/scratch/stefan/7808390/working/building/REAL300025277401 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277401

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277401/0 /scratch/stefan/7808390/working/building/REAL300025277401 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/269
`/scratch/stefan/7808390/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC=C(C#N)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277401 none CCOC=C(C#N)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 192, 172, 192, 192, 162, 172, 162, 162, 162, 162, 127, 162, 76, 76, 32, 76, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 162, 162, 162, 162, 162, 162, 162, 162, 162, 127, 127, 76, 32, 32, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 772
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277401 none CCOC=C(C#N)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 8, 8, 4, 8, 8, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 37, 68, 162, 162, 162, 162, 162, 23, 23, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 37, 37, 162] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 405
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277401 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277401
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277401/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277401
Building REAL300025277402
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277402'
/scratch/stefan/7808390/working/building/REAL300025277402 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277402

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277402/0 /scratch/stefan/7808390/working/building/REAL300025277402 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/270
`/scratch/stefan/7808390/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C#N)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277402 none CC(C)(C#N)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 201, 188, 129, 126, 129, 126, 126, 126, 126, 94, 126, 52, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 126, 126, 126, 126, 126, 126, 126, 126, 126, 94, 94, 52, 30, 30, 1] 201
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 905
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277402 none CC(C)(C#N)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 29, 43, 126, 126, 126, 126, 126, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 29, 29, 126] 201
rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 315
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277402 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277402
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277402/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277402
Building REAL300025277403
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277403'
/scratch/stefan/7808390/working/building/REAL300025277403 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277403

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277403/0 /scratch/stefan/7808390/working/building/REAL300025277403 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/271
`/scratch/stefan/7808390/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1)

`REAL300025277403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277403 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [149, 111, 65, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 184, 184, 201, 201, 201, 201, 201, 201, 149, 149, 149, 111, 111, 65, 30, 30, 1, 149, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 759
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277403 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 12, 12, 12, 41, 60, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 2, 2, 2, 6, 6, 12, 41, 41, 149, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
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: REAL300025277403 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 41, 41, 41, 110, 132, 201, 201, 201, 201, 201, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 41, 110, 110, 201, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 1] 201
rigid atoms, others: [42, 43, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/7808390/working/building/REAL300025277403 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277403
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277403/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277403
Building REAL300025277404
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277404'
/scratch/stefan/7808390/working/building/REAL300025277404 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277404

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277404/0 /scratch/stefan/7808390/working/building/REAL300025277404 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/272
`/scratch/stefan/7808390/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCC1)

`REAL300025277404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277404 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [149, 115, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 165, 165, 201, 201, 201, 201, 149, 149, 149, 115, 115, 68, 30, 30, 1, 149, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 852
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277404 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 39, 56, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 3, 3, 11, 17, 17, 17, 2, 2, 2, 5, 5, 10, 39, 39, 149, 1, 1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 17, 17, 17] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277404 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 51, 51, 51, 113, 135, 201, 201, 201, 201, 201, 17, 17, 17, 13, 6, 13, 1, 1, 1, 1, 1, 17, 17, 17, 32, 32, 51, 113, 113, 201, 17, 17, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 47, 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, 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/7808390/working/building/REAL300025277404 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277404/1 /scratch/stefan/7808390/working/building/REAL300025277404 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/273
`/scratch/stefan/7808390/working/3D/273' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCC1)

`REAL300025277404.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277404/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277404 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [19, 18, 16, 16, 16, 16, 11, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 18, 18, 16, 16, 16, 1, 19, 19, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28] 28
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277404 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 7, 7, 7, 11, 12, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 7, 11, 11, 19, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8] 28
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([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, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277404 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C[NH+]1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 12, 12, 12, 17, 19, 28, 28, 28, 28, 28, 8, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 12, 17, 17, 28, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1] 28
rigid atoms, others: [43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 89
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277404 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277404
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277404/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277404/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277404
Building REAL300025277405
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277405'
/scratch/stefan/7808390/working/building/REAL300025277405 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277405

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277405/0 /scratch/stefan/7808390/working/building/REAL300025277405 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/274
`/scratch/stefan/7808390/working/3D/274' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277405 none CC(C)C(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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, 183, 201, 168, 183, 128, 128, 128, 128, 128, 128, 128, 91, 128, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 183, 549, 168, 168, 128, 128, 128, 128, 128, 128, 128, 128, 128, 91, 91, 48, 29, 29, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1498
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277405 none CC(C)C(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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: [23, 11, 23, 6, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 31, 41, 128, 128, 128, 128, 128, 23, 23, 23, 23, 23, 23, 23, 11, 33, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 31, 31, 128] 603
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 387
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277405 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277405
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277405/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277405
Building REAL300025277406
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277406'
/scratch/stefan/7808390/working/building/REAL300025277406 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277406

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277406/0 /scratch/stefan/7808390/working/building/REAL300025277406 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/275
`/scratch/stefan/7808390/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CCC1)

`REAL300025277406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277406 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [86, 77, 62, 62, 30, 62, 12, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 97, 97, 97, 97, 97, 86, 86, 86, 77, 77, 62, 30, 30, 1, 86, 86, 86, 86, 86, 86, 97, 97, 97, 97, 97, 97] 97
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277406 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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, 5, 12, 12, 12, 40, 52, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 2, 2, 2, 5, 5, 12, 40, 40, 86, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 97
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 239
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: REAL300025277406 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=C(Cl)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 13, 26, 26, 26, 59, 73, 97, 97, 97, 97, 97, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 26, 59, 59, 97, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 97
rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 297
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277406 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277406
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277406/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277406
Building REAL300025277407
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277407'
/scratch/stefan/7808390/working/building/REAL300025277407 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277407

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277407/0 /scratch/stefan/7808390/working/building/REAL300025277407 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/276
`/scratch/stefan/7808390/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1COC(=O)C1)

`REAL300025277407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277407 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1COC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [106, 88, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 107, 107, 127, 127, 127, 127, 127, 106, 106, 106, 88, 88, 62, 29, 29, 1, 106, 106, 106, 106, 106, 106, 127, 127, 127, 127, 127] 127
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277407 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1COC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 14, 14, 14, 51, 58, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 2, 2, 2, 5, 5, 14, 51, 51, 106, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 127
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277407 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1COC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 18, 38, 38, 38, 89, 97, 127, 127, 127, 127, 127, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 38, 89, 89, 127, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 127
rigid atoms, others: [41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 404
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277407 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277407
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277407/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277407
Building REAL300025277408
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277408'
/scratch/stefan/7808390/working/building/REAL300025277408 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277408

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277408/0 /scratch/stefan/7808390/working/building/REAL300025277408 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/277
`/scratch/stefan/7808390/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025277408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277408 none CC1CC=C(C(=O)N2CCCC2(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 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, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 49, 80, 179, 179, 179, 179, 179, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 49, 49, 179, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277408 none CC1CC=C(C(=O)N2CCCC2(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 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, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 9, 9, 9, 22, 46, 46, 46, 118, 150, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 46, 118, 118, 201, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 50, 51, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277408 none CC1CC=C(C(=O)N2CCCC2(C)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 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, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 179, 193, 179, 179, 179, 179, 134, 179, 77, 77, 31, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 179, 179, 179, 179, 179, 134, 134, 77, 31, 31, 1, 201, 201, 201, 201] 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: 767
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277408 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277408
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277408/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277408
Building REAL300025277409
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277409'
/scratch/stefan/7808390/working/building/REAL300025277409 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277409

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277409/0 /scratch/stefan/7808390/working/building/REAL300025277409 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/278
`/scratch/stefan/7808390/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277409 none CC(O)C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
450  conformations in input
total number of sets (complete confs): 450
using faster count positions algorithm for large data
unique positions, atoms: [142, 144, 150, 128, 144, 127, 128, 127, 127, 127, 127, 114, 127, 81, 81, 39, 81, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 450, 144, 144, 144, 144, 127, 127, 127, 127, 127, 127, 127, 127, 127, 114, 114, 81, 39, 39, 1] 450
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])
total number of confs: 1112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277409 none CC(O)C(C)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
450  conformations in input
total number of sets (complete confs): 450
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 10, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 48, 62, 127, 127, 127, 127, 127, 10, 10, 10, 10, 30, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 48, 48, 127] 450
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277409 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277409
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277409/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277409
Building REAL300025277410
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277410'
/scratch/stefan/7808390/working/building/REAL300025277410 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277410

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277410/0 /scratch/stefan/7808390/working/building/REAL300025277410 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/279
`/scratch/stefan/7808390/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1[N-]C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CC1=O)

`REAL300025277410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277410 none CN1[N-]C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [14, 14, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 39, 73, 152, 152, 152, 152, 152, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 39, 39, 152, 14] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 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])
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: REAL300025277410 none CN1[N-]C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 14, 26, 47, 47, 47, 114, 159, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 26, 26, 47, 114, 114, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277410 none CN1[N-]C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [201, 201, 201, 170, 152, 170, 152, 152, 152, 152, 141, 152, 103, 103, 31, 103, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 152, 152, 152, 152, 152, 141, 141, 103, 31, 31, 1, 201] 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])
total number of confs: 680
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277410 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277410
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277410/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277410
Building REAL300025277411
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277411'
/scratch/stefan/7808390/working/building/REAL300025277411 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277411

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277411/0 /scratch/stefan/7808390/working/building/REAL300025277411 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/280
`/scratch/stefan/7808390/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277411 none C=C1CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 50, 59, 98, 98, 98, 98, 98, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 50, 50, 98] 114
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 5, 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])
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: REAL300025277411 none C=C1CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 17, 36, 36, 36, 75, 86, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 36, 75, 75, 114] 114
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 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])
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: REAL300025277411 none C=C1CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 98, 98, 98, 98, 98, 98, 98, 82, 98, 59, 59, 29, 59, 12, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 98, 98, 98, 98, 98, 98, 98, 98, 98, 82, 82, 59, 29, 29, 1] 114
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])
total number of confs: 436
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277411 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277411
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277411/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277411
Building REAL300025277412
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277412'
/scratch/stefan/7808390/working/building/REAL300025277412 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277412

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277412/0 /scratch/stefan/7808390/working/building/REAL300025277412 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/281
`/scratch/stefan/7808390/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC=CC1)

`REAL300025277412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277412 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC=CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 66, 36, 36, 26, 36, 12, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 174, 201, 201, 201, 201, 101, 101, 101, 66, 66, 36, 26, 26, 1, 101, 101, 101, 101, 101, 101, 174, 174, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 889
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277412 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC=CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 22, 30, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 2, 2, 8, 21, 21, 21, 21, 2, 2, 2, 4, 4, 8, 22, 22, 101, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277412 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC=CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 66, 66, 66, 117, 129, 201, 201, 201, 201, 201, 21, 21, 21, 21, 5, 21, 1, 1, 1, 1, 1, 1, 21, 21, 21, 38, 38, 66, 117, 117, 201, 21, 21, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 646
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277412 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277412
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277412/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277412
Building REAL300025277413
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277413'
/scratch/stefan/7808390/working/building/REAL300025277413 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277413

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277413/0 /scratch/stefan/7808390/working/building/REAL300025277413 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/282
`/scratch/stefan/7808390/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1OCCO1)

`REAL300025277413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277413 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1OCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 92, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 130, 130, 201, 201, 201, 201, 201, 121, 121, 121, 92, 92, 58, 30, 30, 1, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277413 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1OCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 28, 39, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 3, 3, 10, 21, 21, 21, 21, 2, 2, 2, 3, 3, 7, 28, 28, 121, 1, 1, 1, 1, 1, 1, 10, 10, 21, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277413 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1OCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 33, 63, 63, 63, 120, 132, 201, 201, 201, 201, 201, 21, 21, 21, 19, 6, 19, 1, 1, 1, 1, 1, 1, 21, 21, 21, 33, 33, 63, 120, 120, 201, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 654
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277413 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277413
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277413/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277413
Building REAL300025277414
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277414'
/scratch/stefan/7808390/working/building/REAL300025277414 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277414

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277414/0 /scratch/stefan/7808390/working/building/REAL300025277414 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/283
`/scratch/stefan/7808390/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(OC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277414 none COC(OC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 13, 11, 13, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 1] 15
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])
total number of confs: 43
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277414 none COC(OC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [6, 3, 2, 3, 7, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 9, 9, 11, 11, 11, 11, 11, 6, 6, 6, 3, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 9, 9, 11] 15
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 65
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277414 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277414
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277414/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277414
Building REAL300025277415
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277415'
/scratch/stefan/7808390/working/building/REAL300025277415 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277415

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277415/0 /scratch/stefan/7808390/working/building/REAL300025277415 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/284
`/scratch/stefan/7808390/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC[N+](=O)[O-])

`REAL300025277415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277415 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [108, 81, 67, 67, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 176, 153, 201, 201, 201, 108, 108, 108, 81, 81, 67, 29, 29, 1, 108, 108, 108, 108, 108, 108, 176, 176, 185, 185, 176, 194] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1012
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277415 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 4, 6, 6, 6, 24, 45, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 2, 2, 6, 6, 11, 19, 19, 2, 2, 2, 4, 4, 6, 24, 24, 108, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277415 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277415
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277415/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277415
Building REAL300025277416
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277416'
/scratch/stefan/7808390/working/building/REAL300025277416 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277416

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277416/0 /scratch/stefan/7808390/working/building/REAL300025277416 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/285
`/scratch/stefan/7808390/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C#N)CC1)

`REAL300025277416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277416 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C#N)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [107, 89, 53, 53, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 108, 108, 180, 201, 201, 201, 201, 107, 107, 107, 89, 89, 53, 25, 25, 1, 107, 107, 107, 107, 107, 107, 180, 180, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 872
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277416 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C#N)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 9, 9, 9, 43, 46, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 3, 3, 9, 21, 21, 21, 21, 2, 2, 2, 3, 3, 9, 43, 43, 107, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 318
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277416 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(C#N)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.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, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 74, 74, 74, 161, 162, 201, 201, 201, 201, 201, 21, 21, 21, 20, 6, 20, 1, 1, 1, 1, 1, 1, 21, 21, 21, 34, 34, 74, 161, 161, 201, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 732
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277416 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277416
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277416/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277416
Building REAL300025277417
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277417'
/scratch/stefan/7808390/working/building/REAL300025277417 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277417

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277417/0 /scratch/stefan/7808390/working/building/REAL300025277417 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/286
`/scratch/stefan/7808390/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277417 none COC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 168, 95, 95, 95, 95, 95, 95, 95, 76, 95, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 192, 192, 168, 168, 95, 95, 95, 95, 95, 95, 95, 95, 95, 76, 76, 63, 30, 30, 1] 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])
total number of confs: 850
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277417 none COC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 25, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 22, 35, 95, 95, 95, 95, 95, 25, 25, 25, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 22, 22, 95] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 278
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277417 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277417
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277417/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277417
Building REAL300025277418
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277418'
/scratch/stefan/7808390/working/building/REAL300025277418 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277418

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277418/0 /scratch/stefan/7808390/working/building/REAL300025277418 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/287
`/scratch/stefan/7808390/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[NH+](CC)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277418 none CC[NH+](CC)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 175, 170, 175, 170, 170, 170, 170, 150, 170, 103, 103, 35, 103, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 170, 170, 170, 170, 170, 170, 170, 150, 150, 103, 35, 35, 1] 201
rigid atoms, others: [56, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 812
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: REAL300025277418 none CC[NH+](CC)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 14, 14, 18, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 36, 65, 170, 170, 170, 170, 170, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 36, 36, 170] 201
rigid atoms, others: [43, 15, 8, 44, 10, 11, 12, 13, 14, 45, 16, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 426
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277418 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277418
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277418/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277418
Building REAL300025277419
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277419'
/scratch/stefan/7808390/working/building/REAL300025277419 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277419

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277419/0 /scratch/stefan/7808390/working/building/REAL300025277419 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/288
`/scratch/stefan/7808390/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOC1)

`REAL300025277419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277419 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 126, 69, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 159, 159, 201, 201, 201, 201, 201, 153, 153, 153, 126, 126, 69, 31, 31, 1, 153, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: REAL300025277419 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 49, 73, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 2, 2, 2, 5, 5, 15, 49, 49, 153, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025277419 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 47, 47, 47, 111, 132, 201, 201, 201, 201, 201, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 47, 111, 111, 201, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 594
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277419 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277419
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277419/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277419
Building REAL300025277420
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277420'
/scratch/stefan/7808390/working/building/REAL300025277420 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277420

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277420/0 /scratch/stefan/7808390/working/building/REAL300025277420 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/289
`/scratch/stefan/7808390/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=NC(N)=N1)

`REAL300025277420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277420 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=NC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 95, 73, 73, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 128, 128, 176, 201, 201, 201, 201, 201, 121, 121, 121, 95, 95, 73, 30, 30, 1, 121, 121, 121, 121, 121, 121, 176, 176, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 785
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277420 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=NC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 7, 7, 7, 27, 43, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 4, 4, 8, 22, 22, 22, 22, 22, 2, 2, 2, 3, 3, 7, 27, 27, 121, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277420 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=NC(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 35, 49, 49, 49, 111, 128, 201, 201, 201, 201, 201, 22, 22, 22, 20, 9, 20, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 35, 35, 49, 111, 111, 201, 22, 22, 22, 22, 22, 22, 9, 9, 1, 1] 201
rigid atoms, others: [44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277420 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277420
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277420/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277420
Building REAL300025277421
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277421'
/scratch/stefan/7808390/working/building/REAL300025277421 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277421

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277421/0 /scratch/stefan/7808390/working/building/REAL300025277421 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/290
`/scratch/stefan/7808390/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1)

`REAL300025277421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277421 none CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 32, 44, 119, 119, 119, 119, 119, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 32, 32, 119, 6] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277421 none CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 6, 6, 6, 6, 6, 6, 13, 24, 24, 24, 70, 86, 141, 141, 141, 141, 141, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 24, 70, 70, 141, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 26] set([0, 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: 425
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277421 none CCC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 141, 141, 141, 141, 125, 119, 125, 119, 119, 119, 119, 86, 119, 51, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 119, 119, 119, 86, 86, 51, 28, 28, 1, 141] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
total number of confs: 891
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277421 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277421
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277421/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277421
Building REAL300025277422
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277422'
/scratch/stefan/7808390/working/building/REAL300025277422 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277422

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277422/0 /scratch/stefan/7808390/working/building/REAL300025277422 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/291
`/scratch/stefan/7808390/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277422 none CC(C)(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 58, 59, 48, 48, 27, 48, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 177, 59, 59, 59, 59, 59, 59, 59, 59, 59, 58, 58, 48, 27, 27, 1] 177
rigid atoms, others: [51, 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, 50])
total number of confs: 395
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: REAL300025277422 none CC(C)(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 38, 42, 59, 59, 59, 59, 59, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 38, 38, 59] 177
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 206
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277422 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277422
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277422/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277422
Building REAL300025277423
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277423'
/scratch/stefan/7808390/working/building/REAL300025277423 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277423

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277423/0 /scratch/stefan/7808390/working/building/REAL300025277423 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/292
`/scratch/stefan/7808390/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCSCC1)

`REAL300025277423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277423 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCSCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 7, 7, 7, 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, 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, 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: [75, 64, 52, 52, 26, 52, 12, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 76, 76, 91, 91, 91, 91, 91, 75, 75, 75, 64, 64, 52, 26, 26, 1, 75, 75, 75, 75, 75, 75, 91, 91, 91, 91, 91, 91, 91, 91, 91] 91
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277423 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCSCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 42, 48, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 2, 2, 2, 5, 5, 13, 42, 42, 75, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 91
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 222
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: REAL300025277423 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCSCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 7, 7, 7, 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, 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, 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: [5, 5, 5, 11, 25, 25, 25, 62, 70, 91, 91, 91, 91, 91, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 25, 62, 62, 91, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 91
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 276
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277423 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277423
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277423/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277423
Building REAL300025277424
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277424'
/scratch/stefan/7808390/working/building/REAL300025277424 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277424

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277424/0 /scratch/stefan/7808390/working/building/REAL300025277424 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/293
`/scratch/stefan/7808390/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCCC1)

`REAL300025277424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277424 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [113, 74, 47, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 124, 124, 181, 181, 201, 201, 201, 201, 113, 113, 113, 74, 74, 47, 28, 28, 1, 113, 113, 113, 113, 113, 113, 181, 543, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1440
number of broken/clashed sets: 118
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277424 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 5, 9, 9, 9, 28, 37, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 3, 3, 9, 9, 16, 16, 16, 16, 2, 2, 2, 5, 5, 9, 28, 28, 113, 1, 1, 1, 1, 1, 1, 9, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 310
number of broken/clashed sets: 118
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277424 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(O)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 33, 52, 52, 52, 105, 118, 201, 201, 201, 201, 201, 16, 16, 16, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 16, 16, 16, 33, 33, 52, 105, 105, 201, 16, 16, 16, 16, 16, 16, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 640
number of broken/clashed sets: 118
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277424 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277424
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277424/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277424
Building REAL300025277425
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277425'
/scratch/stefan/7808390/working/building/REAL300025277425 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277425

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277425/0 /scratch/stefan/7808390/working/building/REAL300025277425 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/294
`/scratch/stefan/7808390/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCO1)

`REAL300025277425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277425 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [132, 93, 56, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 172, 172, 201, 201, 201, 201, 201, 132, 132, 132, 93, 93, 56, 30, 30, 1, 132, 132, 132, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277425 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 31, 45, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 2, 2, 2, 5, 5, 9, 31, 31, 132, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277425 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 27, 53, 53, 53, 121, 141, 201, 201, 201, 201, 201, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 53, 121, 121, 201, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 632
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277425 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277425
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277425/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277425
Building REAL300025277426
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277426'
/scratch/stefan/7808390/working/building/REAL300025277426 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277426

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277426/0 /scratch/stefan/7808390/working/building/REAL300025277426 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/295
`/scratch/stefan/7808390/working/3D/295' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)N1)

`REAL300025277426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277426 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [89, 73, 51, 51, 23, 51, 12, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 108, 108, 108, 108, 89, 89, 89, 73, 73, 51, 23, 23, 1, 89, 89, 89, 89, 89, 89, 108, 108, 108, 108] 108
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 409
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277426 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 15, 15, 15, 46, 52, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 2, 2, 2, 6, 6, 15, 46, 46, 89, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 108
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 250
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: REAL300025277426 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 18, 38, 38, 38, 81, 87, 108, 108, 108, 108, 108, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 38, 81, 81, 108, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 108
rigid atoms, others: [40, 41, 42, 43, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 355
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277426 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277426
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277426/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277426
Building REAL300025277427
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277427'
/scratch/stefan/7808390/working/building/REAL300025277427 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277427

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277427/0 /scratch/stefan/7808390/working/building/REAL300025277427 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/296
`/scratch/stefan/7808390/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CO)=C1)

`REAL300025277427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277427 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CO)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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: [154, 116, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 180, 180, 201, 201, 201, 201, 201, 201, 154, 154, 154, 116, 116, 64, 30, 30, 1, 154, 154, 154, 154, 154, 154, 201, 201, 603, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 1357
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277427 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CO)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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, 5, 9, 9, 9, 35, 53, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 22, 7, 2, 2, 2, 5, 5, 9, 35, 35, 154, 1, 1, 1, 1, 1, 1, 22, 22, 66, 7] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
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: REAL300025277427 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NOC(CO)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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]
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, 13, 28, 28, 28, 91, 116, 201, 201, 201, 201, 201, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 13, 13, 28, 91, 91, 201, 7, 7, 7, 7, 7, 7, 8, 8, 24, 1] 603
rigid atoms, others: [45, 18, 20, 21, 22, 23, 24, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 27, 28, 29, 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.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277427 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277427
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277427/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277427
Building REAL300025277428
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277428'
/scratch/stefan/7808390/working/building/REAL300025277428 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277428

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277428/0 /scratch/stefan/7808390/working/building/REAL300025277428 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/297
`/scratch/stefan/7808390/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC(=O)N1)

`REAL300025277428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277428 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [66, 53, 40, 40, 25, 40, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 88, 88, 88, 88, 88, 66, 66, 66, 53, 53, 40, 25, 25, 1, 66, 66, 66, 66, 66, 66, 88, 88, 88] 88
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 337
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277428 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 10, 10, 10, 34, 37, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 2, 2, 2, 3, 3, 10, 34, 34, 66, 1, 1, 1, 1, 1, 1, 6, 6, 6] 88
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([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, 41, 42, 43])
total number of confs: 189
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: REAL300025277428 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 11, 31, 31, 31, 66, 72, 88, 88, 88, 88, 88, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 31, 66, 66, 88, 6, 6, 6, 6, 6, 6, 1, 1, 1] 88
rigid atoms, others: [41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 302
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277428 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277428
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277428/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277428
Building REAL300025277429
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277429'
/scratch/stefan/7808390/working/building/REAL300025277429 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277429

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277429/0 /scratch/stefan/7808390/working/building/REAL300025277429 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/298
`/scratch/stefan/7808390/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCC1)

`REAL300025277429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277429 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 128, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 187, 187, 201, 201, 201, 201, 201, 175, 175, 175, 128, 128, 68, 28, 28, 1, 175, 175, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 761
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277429 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 16, 16, 16, 50, 82, 175, 175, 175, 175, 175, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 2, 2, 2, 6, 6, 16, 50, 50, 175, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 407
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: REAL300025277429 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 51, 51, 51, 120, 155, 201, 201, 201, 201, 201, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 51, 120, 120, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 611
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277429 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277429
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277429/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277429
Building REAL300025277430
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277430'
/scratch/stefan/7808390/working/building/REAL300025277430 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277430

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277430/0 /scratch/stefan/7808390/working/building/REAL300025277430 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/299
`/scratch/stefan/7808390/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C(N)=N1)

`REAL300025277430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277430 none CN1C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 37, 49, 136, 136, 136, 136, 136, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 37, 37, 136, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 297
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277430 none CN1C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in 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, 11, 11, 11, 11, 11, 11, 23, 44, 44, 44, 108, 126, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 44, 108, 108, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 46, 47, 24, 25, 26, 30] set([5, 6, 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, 45])
total number of confs: 604
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: REAL300025277430 none CN1C=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)C(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 164, 136, 164, 136, 136, 136, 136, 109, 136, 56, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 136, 136, 136, 136, 136, 136, 136, 136, 136, 109, 109, 56, 31, 31, 1, 201, 201] 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])
total number of confs: 720
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277430 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277430
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277430/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277430
Building REAL300025277431
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277431'
/scratch/stefan/7808390/working/building/REAL300025277431 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277431

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277431/0 /scratch/stefan/7808390/working/building/REAL300025277431 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/300
`/scratch/stefan/7808390/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277431 none CCC[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 175, 130, 175, 175, 124, 130, 124, 124, 124, 124, 86, 124, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 525, 124, 124, 124, 124, 124, 124, 124, 124, 124, 86, 86, 51, 29, 29, 1] 603
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])
total number of confs: 1421
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277431 none CCC[C@H](O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 7, 3, 7, 7, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 32, 44, 124, 124, 124, 124, 124, 17, 17, 17, 17, 17, 17, 17, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 32, 32, 124] 603
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 349
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277431 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277431
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277431/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277431
Building REAL300025277432
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277432'
/scratch/stefan/7808390/working/building/REAL300025277432 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277432

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277432/0 /scratch/stefan/7808390/working/building/REAL300025277432 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/301
`/scratch/stefan/7808390/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1COCCO1)

`REAL300025277432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277432 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1COCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 77, 45, 45, 27, 45, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 189, 201, 201, 201, 201, 201, 113, 113, 113, 77, 77, 45, 27, 27, 1, 113, 113, 113, 113, 113, 113, 189, 189, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277432 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1COCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  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, 9, 9, 9, 27, 36, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 2, 2, 8, 20, 20, 20, 20, 20, 2, 2, 2, 4, 4, 9, 27, 27, 113, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277432 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1COCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 34, 61, 61, 61, 110, 123, 201, 201, 201, 201, 201, 20, 20, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 34, 34, 61, 110, 110, 201, 20, 20, 20, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 625
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277432 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277432
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277432/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277432
Building REAL300025277433
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277433'
/scratch/stefan/7808390/working/building/REAL300025277433 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277433

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277433/0 /scratch/stefan/7808390/working/building/REAL300025277433 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/302
`/scratch/stefan/7808390/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=CC=C1N)

`REAL300025277433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277433 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=CC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 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, 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: [152, 110, 68, 68, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 156, 156, 192, 201, 201, 201, 201, 201, 152, 152, 152, 110, 110, 68, 29, 29, 1, 152, 152, 152, 152, 152, 152, 192, 192, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 818
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277433 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=CC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 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, 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, 5, 10, 10, 10, 33, 51, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 2, 2, 2, 5, 5, 10, 33, 33, 152, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 322
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: REAL300025277433 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1N=CC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 21, 44, 44, 44, 99, 122, 201, 201, 201, 201, 201, 12, 12, 12, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 44, 99, 99, 201, 12, 12, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 585
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277433 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277433
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277433/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277433
Building REAL300025277434
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277434'
/scratch/stefan/7808390/working/building/REAL300025277434 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277434

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277434/0 /scratch/stefan/7808390/working/building/REAL300025277434 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/303
`/scratch/stefan/7808390/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1)

`REAL300025277434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277434 none CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 35, 117, 117, 117, 117, 117, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 24, 24, 117, 6, 6] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 306
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277434 none CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 4, 6, 6, 6, 6, 6, 6, 9, 21, 21, 21, 64, 83, 156, 156, 156, 156, 156, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 21, 64, 64, 156, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 47, 48, 25, 26] set([0, 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: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277434 none CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=CN1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 156, 156, 156, 143, 117, 143, 117, 117, 117, 117, 79, 117, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 117, 117, 117, 79, 79, 50, 26, 26, 1, 156, 156] 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])
total number of confs: 856
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277434 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277434/1 /scratch/stefan/7808390/working/building/REAL300025277434 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/304
`/scratch/stefan/7808390/working/3D/304' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N1)

`REAL300025277434.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277434/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277434 none CCC1=NC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 32, 49, 146, 146, 146, 146, 146, 7, 20, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 32, 32, 146, 7] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 353
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277434 none CCC1=NC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 10, 15, 15, 15, 46, 69, 175, 175, 175, 175, 175, 1, 9, 9, 9, 9, 9, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 15, 46, 46, 175, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 391
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: REAL300025277434 none CCC1=NC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need 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, 175, 175, 175, 162, 146, 162, 146, 146, 146, 146, 101, 146, 67, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 175, 201, 201, 201, 201, 201, 175, 146, 146, 146, 146, 146, 146, 146, 146, 146, 101, 101, 67, 30, 30, 1, 175] 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])
total number of confs: 816
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277434 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277434
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277434/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277434/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277434
Building REAL300025277435
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277435'
/scratch/stefan/7808390/working/building/REAL300025277435 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277435

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277435/0 /scratch/stefan/7808390/working/building/REAL300025277435 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/305
`/scratch/stefan/7808390/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1)

`REAL300025277435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277435 none CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 23, 35, 111, 111, 111, 111, 111, 7, 7, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 23, 23, 111, 7] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277435 none CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 10, 20, 20, 20, 59, 84, 167, 167, 167, 167, 167, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20, 59, 59, 167, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 47, 25, 26] set([0, 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: 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: REAL300025277435 none CCC1=NC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=NN1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need 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, 111, 111, 111, 111, 111, 111, 111, 77, 111, 48, 48, 27, 48, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 111, 111, 111, 111, 77, 77, 48, 27, 27, 1, 167] 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])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277435 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277435/1 /scratch/stefan/7808390/working/building/REAL300025277435 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/306
`/scratch/stefan/7808390/working/3D/306' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NNC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277435.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277435/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277435 none CCC1=NNC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 33, 44, 132, 132, 132, 132, 132, 6, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 33, 33, 132] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277435 none CCC1=NNC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 4, 4, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 67, 83, 163, 163, 163, 163, 163, 1, 8, 8, 8, 8, 8, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 67, 67, 163] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 458
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277435 none CCC1=NNC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 163, 163, 163, 163, 155, 132, 155, 132, 132, 132, 132, 96, 132, 53, 53, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 163, 201, 201, 201, 201, 201, 163, 132, 132, 132, 132, 132, 132, 132, 132, 132, 96, 96, 53, 26, 26, 1] 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])
total number of confs: 861
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277435 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277435
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277435/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277435/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277435
Building REAL300025277436
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277436'
/scratch/stefan/7808390/working/building/REAL300025277436 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277436

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277436/0 /scratch/stefan/7808390/working/building/REAL300025277436 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/307
`/scratch/stefan/7808390/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCOC1)

`REAL300025277436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277436 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 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: [181, 128, 62, 62, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 184, 184, 201, 201, 201, 201, 201, 201, 181, 181, 181, 128, 128, 62, 31, 31, 1, 181, 181, 181, 181, 181, 181, 201, 201, 603, 201, 201, 201, 201, 201, 201] 603
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 1433
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277436 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 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, 5, 15, 15, 15, 48, 67, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 3, 3, 9, 13, 13, 13, 13, 13, 2, 2, 2, 5, 5, 15, 48, 48, 181, 1, 1, 1, 1, 1, 1, 9, 9, 39, 13, 13, 13, 13, 13, 13] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 459
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277436 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(O)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 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, 13, 13, 25, 52, 52, 52, 116, 142, 201, 201, 201, 201, 201, 13, 13, 13, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 52, 116, 116, 201, 13, 13, 13, 13, 13, 13, 4, 4, 6, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [45, 46, 47, 48, 49, 50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/7808390/working/building/REAL300025277436 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277436
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277436/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277436
Building REAL300025277437
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277437'
/scratch/stefan/7808390/working/building/REAL300025277437 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277437

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277437/0 /scratch/stefan/7808390/working/building/REAL300025277437 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/308
`/scratch/stefan/7808390/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CN=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277437 none CN1N=CN=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 15, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 49, 69, 161, 161, 161, 161, 161, 15, 15, 15, 15, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 15, 49, 49, 161] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 402
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277437 none CN1N=CN=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 15, 15, 15, 15, 15, 15, 25, 45, 45, 45, 108, 131, 201, 201, 201, 201, 201, 2, 2, 2, 1, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 25, 25, 45, 108, 108, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30] set([7, 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])
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: REAL300025277437 none CN1N=CN=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 168, 161, 168, 161, 161, 161, 161, 130, 161, 70, 70, 30, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 161, 161, 161, 161, 161, 161, 161, 161, 161, 130, 130, 70, 30, 30, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 822
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277437 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277437
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277437/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277437
Building REAL300025277438
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277438'
/scratch/stefan/7808390/working/building/REAL300025277438 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277438

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277438/0 /scratch/stefan/7808390/working/building/REAL300025277438 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/309
`/scratch/stefan/7808390/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277438 none CC1=NN(C)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 53, 68, 164, 164, 164, 164, 164, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 53, 53, 164] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277438 none CC1=NN(C)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 9, 9, 9, 9, 9, 9, 23, 50, 50, 50, 106, 125, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 50, 106, 106, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([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, 47])
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: REAL300025277438 none CC1=NN(C)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 164, 181, 164, 164, 164, 164, 122, 164, 58, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 164, 164, 164, 164, 122, 122, 58, 29, 29, 1] 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])
total number of confs: 735
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277438 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277438
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277438/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277438
Building REAL300025277439
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277439'
/scratch/stefan/7808390/working/building/REAL300025277439 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277439

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277439/0 /scratch/stefan/7808390/working/building/REAL300025277439 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/310
`/scratch/stefan/7808390/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CCC1)

`REAL300025277439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277439 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7] 7
rigid atoms, others: [45, 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, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277439 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 4, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 7, 3, 3, 3, 3, 3, 3] 7
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 36, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277439 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+]1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 7, 1, 1, 1, 1, 1, 1] 7
rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 22
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277439 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277439/1 /scratch/stefan/7808390/working/building/REAL300025277439 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/311
`/scratch/stefan/7808390/working/3D/311' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CCC1)

`REAL300025277439.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277439/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277439 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 167, 180, 167, 167, 167, 167, 128, 167, 71, 71, 31, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 167, 167, 167, 167, 167, 167, 128, 128, 71, 31, 31, 1, 201, 201, 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])
total number of confs: 829
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277439 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 43, 67, 167, 167, 167, 167, 167, 9, 11, 11, 11, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 43, 43, 167, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 30, 31] set([0, 1, 3, 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])
total number of confs: 379
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277439 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)N1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 9, 11, 11, 11, 11, 11, 11, 23, 47, 47, 47, 114, 138, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 47, 114, 114, 201, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 45, 46, 47, 48, 49, 50, 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, 42, 43, 44])
total number of confs: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277439 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277439
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277439/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277439/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277439
Building REAL300025277440
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277440'
/scratch/stefan/7808390/working/building/REAL300025277440 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277440

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277440/0 /scratch/stefan/7808390/working/building/REAL300025277440 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/312
`/scratch/stefan/7808390/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1)

`REAL300025277440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277440 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [189, 150, 84, 84, 33, 84, 13, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 150, 150, 84, 33, 33, 1, 189, 189, 189, 189, 189, 189, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 780
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277440 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 6, 15, 15, 15, 57, 91, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 4, 4, 7, 7, 4, 5, 7, 7, 2, 2, 2, 6, 6, 15, 57, 57, 189, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 459
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: REAL300025277440 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(N)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [7, 7, 7, 19, 41, 41, 41, 108, 139, 201, 201, 201, 201, 201, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 41, 108, 108, 201, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 1, 1] 201
rigid atoms, others: [42, 43, 46, 47, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45])
total number of confs: 606
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277440 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277440
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277440/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277440
Building REAL300025277441
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277441'
/scratch/stefan/7808390/working/building/REAL300025277441 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277441

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277441/0 /scratch/stefan/7808390/working/building/REAL300025277441 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/313
`/scratch/stefan/7808390/working/3D/313' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC1(F)F)

`REAL300025277441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277441 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC1(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [123, 104, 72, 72, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 124, 124, 139, 139, 139, 139, 139, 123, 123, 123, 104, 104, 72, 31, 31, 1, 123, 123, 123, 123, 123, 123, 139, 139] 139
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025277441 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC1(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [1, 1, 1, 5, 15, 15, 15, 55, 66, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 15, 55, 55, 123, 1, 1, 1, 1, 1, 1, 9, 9] 139
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
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: REAL300025277441 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC1(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 18, 39, 39, 39, 89, 105, 139, 139, 139, 139, 139, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 39, 89, 89, 139, 9, 9, 9, 9, 9, 9, 1, 1] 139
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 426
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277441 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277441
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277441/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277441
Building REAL300025277442
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277442'
/scratch/stefan/7808390/working/building/REAL300025277442 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277442

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277442/0 /scratch/stefan/7808390/working/building/REAL300025277442 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/314
`/scratch/stefan/7808390/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNN=C1)

`REAL300025277442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277442 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [45, 39, 32, 32, 24, 32, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 52, 52, 52, 52, 52, 45, 45, 45, 39, 39, 32, 24, 24, 1, 45, 45, 45, 45, 45, 45, 52, 52, 52, 52, 52] 52
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277442 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 6, 6, 6, 16, 19, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 2, 2, 6, 7, 7, 7, 7, 2, 2, 2, 3, 3, 6, 16, 16, 45, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7] 52
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277442 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 10, 13, 13, 13, 27, 31, 54, 54, 54, 54, 54, 6, 6, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 13, 27, 27, 54, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1] 54
rigid atoms, others: [43, 44, 45, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 172
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277442 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277442
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277442/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277442
Building REAL300025277443
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277443'
/scratch/stefan/7808390/working/building/REAL300025277443 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277443

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277443/0 /scratch/stefan/7808390/working/building/REAL300025277443 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/315
`/scratch/stefan/7808390/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=C1)

`REAL300025277443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277443 none CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 42, 61, 149, 149, 149, 149, 149, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 13, 42, 42, 149, 9] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277443 none CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 9, 9, 9, 20, 41, 41, 41, 113, 138, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 41, 113, 113, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 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: 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: REAL300025277443 none CC1=CC=C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)N=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 149, 187, 149, 149, 149, 149, 112, 149, 63, 63, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 149, 149, 149, 149, 112, 112, 63, 31, 31, 1, 201] 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])
total number of confs: 781
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277443 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277443
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277443/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277443
Building REAL300025277444
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277444'
/scratch/stefan/7808390/working/building/REAL300025277444 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277444

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277444/0 /scratch/stefan/7808390/working/building/REAL300025277444 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/316
`/scratch/stefan/7808390/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC(=O)NN1)

`REAL300025277444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277444 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC(=O)NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [89, 67, 48, 48, 27, 48, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 165, 201, 201, 201, 201, 201, 89, 89, 89, 67, 67, 48, 27, 27, 1, 89, 89, 89, 89, 89, 89, 165, 165, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277444 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC(=O)NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 21, 28, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 2, 2, 8, 22, 22, 22, 22, 22, 2, 2, 2, 3, 3, 7, 21, 21, 89, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277444 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC(=O)NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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, 22, 22, 35, 49, 49, 49, 92, 111, 201, 201, 201, 201, 201, 22, 22, 22, 22, 8, 22, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 35, 35, 49, 92, 92, 201, 22, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 604
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277444 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277444
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277444/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277444
Building REAL300025277445
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277445'
/scratch/stefan/7808390/working/building/REAL300025277445 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277445

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277445/0 /scratch/stefan/7808390/working/building/REAL300025277445 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/317
`/scratch/stefan/7808390/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277445 none CC(C)(C)CC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 130, 201, 122, 130, 122, 122, 122, 122, 87, 122, 51, 51, 27, 51, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 122, 122, 122, 122, 122, 122, 122, 122, 122, 87, 87, 51, 27, 27, 1] 603
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 1495
number of broken/clashed sets: 603
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277445 none CC(C)(C)CC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 13, 11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 36, 51, 122, 122, 122, 122, 122, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 33, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 36, 36, 122] 603
rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 348
number of broken/clashed sets: 603
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277445 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277445
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277445/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277445
Building REAL300025277446
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277446'
/scratch/stefan/7808390/working/building/REAL300025277446 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277446

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277446/0 /scratch/stefan/7808390/working/building/REAL300025277446 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/318
`/scratch/stefan/7808390/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNC=C1)

`REAL300025277446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277446 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [85, 67, 45, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 113, 139, 139, 139, 139, 85, 85, 85, 67, 67, 45, 29, 29, 1, 85, 85, 85, 85, 85, 85, 113, 113, 139, 139, 139, 139] 139
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277446 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [1, 1, 1, 3, 8, 8, 8, 24, 31, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 2, 2, 7, 14, 14, 14, 14, 2, 2, 2, 3, 3, 8, 24, 24, 85, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14] 139
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46])
total number of confs: 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: REAL300025277446 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CNC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [14, 14, 14, 26, 39, 39, 39, 79, 85, 139, 139, 139, 139, 139, 14, 14, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 39, 79, 79, 139, 14, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1] 139
rigid atoms, others: [43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 452
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277446 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277446
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277446/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277446
Building REAL300025277447
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277447'
/scratch/stefan/7808390/working/building/REAL300025277447 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277447

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277447/0 /scratch/stefan/7808390/working/building/REAL300025277447 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/319
`/scratch/stefan/7808390/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277447 none COC(=O)C(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 184, 201, 165, 184, 116, 116, 116, 116, 116, 116, 116, 90, 116, 70, 70, 29, 70, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 184, 184, 184, 184, 165, 165, 116, 116, 116, 116, 116, 116, 116, 116, 116, 90, 90, 70, 29, 29, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 856
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: REAL300025277447 none COC(=O)C(C)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 20, 7, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 21, 38, 116, 116, 116, 116, 116, 20, 20, 20, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 21, 21, 116] 201
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 300
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277447 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277447
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277447/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277447
Building REAL300025277448
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277448'
/scratch/stefan/7808390/working/building/REAL300025277448 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277448

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277448/0 /scratch/stefan/7808390/working/building/REAL300025277448 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/320
`/scratch/stefan/7808390/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1)

`REAL300025277448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277448 none CC1(C)CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 46, 70, 154, 154, 154, 154, 154, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 13, 46, 46, 154] 201
rigid atoms, others: [43, 6, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277448 none CC1(C)CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 11, 22, 42, 42, 42, 110, 131, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 42, 110, 110, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 35, 36, 26, 37] set([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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277448 none CC1(C)CCC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)O1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 170, 154, 170, 154, 154, 154, 154, 120, 154, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 154, 154, 154, 154, 120, 120, 64, 30, 30, 1] 201
rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] 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, 50, 51])
total number of confs: 779
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277448 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277448
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277448/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277448
Building REAL300025277449
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277449'
/scratch/stefan/7808390/working/building/REAL300025277449 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277449

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277449/0 /scratch/stefan/7808390/working/building/REAL300025277449 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/321
`/scratch/stefan/7808390/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277449 none CN1N=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 22, 28, 88, 88, 88, 88, 88, 18, 18, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 22, 22, 88] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277449 none CN1N=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 18, 18, 18, 18, 18, 18, 30, 49, 49, 49, 99, 115, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 49, 99, 99, 201] 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, 47, 48])
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: REAL300025277449 none CN1N=CC=C1CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 95, 88, 95, 88, 88, 88, 88, 57, 88, 36, 36, 24, 36, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 175, 88, 88, 88, 88, 88, 88, 88, 88, 88, 57, 57, 36, 24, 24, 1] 201
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 806
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277449 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277449
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277449/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277449
Building REAL300025277450
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277450'
/scratch/stefan/7808390/working/building/REAL300025277450 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277450

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277450/0 /scratch/stefan/7808390/working/building/REAL300025277450 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/322
`/scratch/stefan/7808390/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)C1)

`REAL300025277450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277450 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 80, 40, 40, 25, 40, 12, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 116, 116, 169, 201, 201, 201, 201, 115, 115, 115, 80, 80, 40, 25, 25, 1, 115, 115, 115, 115, 115, 115, 169, 169, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 888
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277450 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 27, 31, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 3, 3, 9, 21, 21, 21, 21, 2, 2, 2, 4, 4, 8, 27, 27, 115, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277450 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 72, 72, 72, 131, 141, 201, 201, 201, 201, 201, 21, 21, 21, 20, 6, 20, 1, 1, 1, 1, 1, 1, 21, 21, 21, 40, 40, 72, 131, 131, 201, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 679
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277450 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277450
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277450/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277450
Building REAL300025277451
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277451'
/scratch/stefan/7808390/working/building/REAL300025277451 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277451

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277451/0 /scratch/stefan/7808390/working/building/REAL300025277451 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/323
`/scratch/stefan/7808390/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CSC1)

`REAL300025277451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277451 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 100, 59, 59, 26, 59, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 117, 117, 174, 201, 201, 201, 116, 116, 116, 100, 100, 59, 26, 26, 1, 116, 116, 116, 116, 116, 116, 174, 174, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277451 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 9, 9, 9, 46, 48, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 2, 2, 8, 23, 23, 23, 2, 2, 2, 3, 3, 9, 46, 46, 116, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 23] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277451 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 77, 77, 77, 167, 170, 201, 201, 201, 201, 201, 23, 23, 23, 22, 6, 22, 1, 1, 1, 1, 1, 23, 23, 23, 39, 39, 77, 167, 167, 201, 23, 23, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 741
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277451 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277451
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277451/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277451
Building REAL300025277452
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277452'
/scratch/stefan/7808390/working/building/REAL300025277452 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277452

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277452/0 /scratch/stefan/7808390/working/building/REAL300025277452 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/324
`/scratch/stefan/7808390/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC=N1)

`REAL300025277452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277452 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [184, 158, 103, 103, 35, 103, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 190, 190, 193, 193, 193, 193, 184, 184, 184, 158, 158, 103, 35, 35, 1, 184, 184, 184, 184, 184, 184, 193, 193, 193] 193
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 711
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277452 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 7, 20, 20, 20, 82, 106, 184, 184, 184, 184, 184, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 2, 2, 2, 7, 7, 20, 82, 82, 184, 1, 1, 1, 1, 1, 1, 9, 9, 9] 193
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 479
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277452 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CNC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [9, 9, 9, 21, 53, 53, 53, 129, 152, 193, 193, 193, 193, 193, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 53, 129, 129, 193, 9, 9, 9, 9, 9, 9, 1, 1, 1] 193
rigid atoms, others: [40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 604
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277452 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277452/1 /scratch/stefan/7808390/working/building/REAL300025277452 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/325
`/scratch/stefan/7808390/working/3D/325' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CN1)

`REAL300025277452.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277452/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277452 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 25, 23, 23, 15, 23, 10, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 23, 15, 15, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 91
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277452 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 9, 9, 9, 20, 22, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 2, 2, 2, 3, 3, 9, 20, 20, 27, 1, 1, 1, 1, 1, 1, 7, 7, 7] 27
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 104
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277452 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 9, 15, 15, 15, 24, 25, 27, 27, 27, 27, 27, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 15, 24, 24, 27, 7, 7, 7, 7, 7, 7, 1, 1, 1] 27
rigid atoms, others: [40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 93
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277452 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277452
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277452/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277452/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277452
Building REAL300025277453
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277453'
/scratch/stefan/7808390/working/building/REAL300025277453 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277453

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277453/0 /scratch/stefan/7808390/working/building/REAL300025277453 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/326
`/scratch/stefan/7808390/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277453 none CC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 44, 63, 145, 145, 145, 145, 145, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 44, 44, 145] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025277453 none CC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 13, 13, 13, 13, 13, 13, 30, 57, 57, 57, 114, 135, 201, 201, 201, 201, 201, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30, 30, 57, 114, 114, 201] 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: 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: REAL300025277453 none CC1=NOC(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 145, 175, 145, 145, 145, 145, 112, 145, 57, 57, 31, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 145, 145, 145, 145, 145, 145, 145, 145, 145, 112, 112, 57, 31, 31, 1] 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])
total number of confs: 753
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277453 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277453
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277453/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277453
Building REAL300025277454
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277454'
/scratch/stefan/7808390/working/building/REAL300025277454 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277454

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277454/0 /scratch/stefan/7808390/working/building/REAL300025277454 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/327
`/scratch/stefan/7808390/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277454 none CCOC(=O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 145, 200, 113, 113, 113, 113, 113, 113, 113, 80, 113, 57, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 113, 113, 113, 113, 113, 113, 113, 113, 113, 80, 80, 57, 29, 29, 1] 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])
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: REAL300025277454 none CCOC(=O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 24, 39, 113, 113, 113, 113, 113, 18, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 24, 24, 113] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277454 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277454
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277454/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277454
Building REAL300025277455
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277455'
/scratch/stefan/7808390/working/building/REAL300025277455 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277455

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277455/0 /scratch/stefan/7808390/working/building/REAL300025277455 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/328
`/scratch/stefan/7808390/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)C1)

`REAL300025277455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277455 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [117, 96, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 118, 118, 148, 148, 148, 148, 117, 117, 117, 96, 96, 62, 30, 30, 1, 117, 117, 117, 117, 117, 117, 148, 148, 148, 148, 148] 148
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 565
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277455 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 16, 16, 16, 57, 66, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 2, 2, 2, 5, 5, 16, 57, 57, 117, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 148
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44])
total number of confs: 321
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277455 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 18, 44, 44, 44, 108, 119, 148, 148, 148, 148, 148, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 44, 108, 108, 148, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 148
rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 484
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277455 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277455
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277455/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277455
Building REAL300025277456
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277456'
/scratch/stefan/7808390/working/building/REAL300025277456 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277456

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277456/0 /scratch/stefan/7808390/working/building/REAL300025277456 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/329
`/scratch/stefan/7808390/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=CN=N1)

`REAL300025277456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277456 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [162, 130, 80, 80, 31, 80, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 165, 165, 201, 201, 201, 201, 201, 162, 162, 162, 130, 130, 80, 31, 31, 1, 162, 162, 162, 162, 162, 162, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277456 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 11, 11, 11, 42, 69, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 3, 3, 10, 17, 17, 17, 17, 2, 2, 2, 5, 5, 11, 42, 42, 162, 1, 1, 1, 1, 1, 1, 10, 10, 17, 17] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277456 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 31, 52, 52, 52, 124, 152, 201, 201, 201, 201, 201, 17, 17, 17, 15, 6, 15, 1, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 52, 124, 124, 201, 17, 17, 17, 17, 17, 17, 6, 6, 1, 1] 201
rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 653
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277456 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277456
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277456/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277456
Building REAL300025277457
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277457'
/scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277457

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277457/0 /scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/330
`/scratch/stefan/7808390/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277457 none C[N@@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 57, 76, 131, 131, 131, 131, 131, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 17, 57, 57, 131] 145
rigid atoms, others: [45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 17, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277457 none C[N@@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 16, 34, 34, 34, 81, 97, 145, 145, 145, 145, 145, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 34, 81, 81, 145] 145
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 7, 8, 9, 39, 34, 35, 32, 36, 38, 37, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 432
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277457 none C[N@@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 145, 145, 145, 145, 145, 133, 145, 131, 133, 131, 131, 131, 131, 117, 131, 69, 69, 29, 69, 10, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 131, 131, 131, 131, 131, 131, 131, 131, 131, 117, 117, 69, 29, 29, 1] 145
rigid atoms, others: [54, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 574
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277457/1 /scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/331
`/scratch/stefan/7808390/working/3D/331' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277457.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277457/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277457 none C[N@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 19, 22, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 19, 19, 41] 41
rigid atoms, others: [45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 17, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277457 none C[N@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 9, 17, 17, 17, 23, 26, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 17, 23, 23, 41] 41
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 7, 8, 9, 39, 34, 35, 32, 36, 38, 37, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277457 none C[N@H+]1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 39, 41, 29, 29, 21, 29, 11, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 39, 39, 29, 21, 21, 1] 41
rigid atoms, others: [54, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 160
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277457/2 /scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/332
`/scratch/stefan/7808390/working/3D/332' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277457.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277457/2/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: REAL300025277457 none CN1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 7, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 58, 86, 173, 173, 173, 173, 173, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 17, 58, 58, 173] 201
rigid atoms, others: [43, 39, 8, 41, 10, 11, 12, 13, 14, 44, 16, 40, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277457 none CN1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 7, 7, 7, 7, 7, 7, 17, 37, 37, 37, 101, 132, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 37, 101, 101, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 35, 36, 38, 5, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 568
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277457 none CN1CCCC[C@@H]1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 201, 173, 197, 173, 173, 173, 173, 137, 173, 80, 80, 31, 80, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 173, 173, 173, 173, 173, 137, 137, 80, 31, 31, 1] 201
rigid atoms, others: [21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 777
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277457 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277457
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277457/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277457/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277457/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277457
Building REAL300025277458
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277458'
/scratch/stefan/7808390/working/building/REAL300025277458 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277458

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277458/0 /scratch/stefan/7808390/working/building/REAL300025277458 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/333
`/scratch/stefan/7808390/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277458 none CCC(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 179, 201, 120, 179, 110, 120, 110, 110, 110, 110, 77, 110, 47, 47, 28, 47, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 537, 110, 110, 110, 110, 110, 110, 110, 110, 110, 77, 77, 47, 28, 28, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1462
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: REAL300025277458 none CCC(C)C(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 19, 10, 19, 3, 10, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 29, 40, 110, 110, 110, 110, 110, 21, 21, 21, 21, 21, 19, 19, 19, 19, 10, 30, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 29, 29, 110] 603
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 358
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277458 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277458
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277458/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277458
Building REAL300025277459
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277459'
/scratch/stefan/7808390/working/building/REAL300025277459 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277459

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277459/0 /scratch/stefan/7808390/working/building/REAL300025277459 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/334
`/scratch/stefan/7808390/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)=C1CC1)

`REAL300025277459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277459 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 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, 139, 136, 139, 136, 136, 136, 136, 121, 136, 81, 81, 36, 81, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 136, 136, 136, 136, 136, 136, 136, 136, 136, 121, 121, 81, 36, 36, 1, 177, 177, 177, 177] 177
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: 684
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277459 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 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: [10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 57, 73, 136, 136, 136, 136, 136, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 57, 57, 136, 10, 10, 10, 10] 177
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 3, 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: 359
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: REAL300025277459 none CC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 21, 47, 47, 47, 112, 128, 177, 177, 177, 177, 177, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 47, 112, 112, 177, 1, 1, 1, 1] 177
rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 22, 23, 24] set([3, 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, 38, 39, 40, 41, 42])
total number of confs: 559
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277459 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277459
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277459/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277459
Building REAL300025277460
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277460'
/scratch/stefan/7808390/working/building/REAL300025277460 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277460

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277460/0 /scratch/stefan/7808390/working/building/REAL300025277460 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/335
`/scratch/stefan/7808390/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277460 none CC1=CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 48, 56, 112, 112, 112, 112, 112, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 48, 48, 112] 157
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 5, 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])
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: REAL300025277460 none CC1=CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 17, 39, 39, 39, 104, 121, 157, 157, 157, 157, 157, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 39, 104, 104, 157] 157
rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277460 none CC1=CC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 113, 112, 113, 112, 112, 112, 112, 94, 112, 69, 69, 32, 69, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 112, 112, 112, 112, 112, 112, 112, 112, 112, 94, 94, 69, 32, 32, 1] 157
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])
total number of confs: 599
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277460 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277460
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277460/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277460
Building REAL300025277461
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277461'
/scratch/stefan/7808390/working/building/REAL300025277461 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277461

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277461/0 /scratch/stefan/7808390/working/building/REAL300025277461 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/336
`/scratch/stefan/7808390/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277461 none CN(C)C(=O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 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, 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, 94, 107, 93, 94, 93, 93, 93, 93, 85, 93, 60, 60, 32, 60, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 93, 93, 93, 93, 93, 93, 93, 93, 93, 85, 85, 60, 32, 32, 1] 107
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])
total number of confs: 415
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277461 none CN(C)C(=O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 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, 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: [7, 6, 7, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 45, 50, 93, 93, 93, 93, 93, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 45, 45, 93] 107
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 273
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277461 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277461
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277461/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277461
Building REAL300025277462
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277462'
/scratch/stefan/7808390/working/building/REAL300025277462 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277462

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277462/0 /scratch/stefan/7808390/working/building/REAL300025277462 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/337
`/scratch/stefan/7808390/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277462 none CCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 178, 133, 178, 126, 133, 126, 126, 126, 126, 87, 126, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 178, 534, 126, 126, 126, 126, 126, 126, 126, 126, 126, 87, 87, 51, 29, 29, 1] 603
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])
total number of confs: 1429
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277462 none CCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 32, 44, 126, 126, 126, 126, 126, 17, 17, 17, 17, 17, 17, 17, 7, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 32, 32, 126] 603
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 350
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277462 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277462
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277462/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277462
Building REAL300025277463
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277463'
/scratch/stefan/7808390/working/building/REAL300025277463 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277463

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277463/0 /scratch/stefan/7808390/working/building/REAL300025277463 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/338
`/scratch/stefan/7808390/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277463 none CCCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 174, 115, 174, 106, 115, 106, 106, 106, 106, 71, 106, 45, 45, 28, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 522, 106, 106, 106, 106, 106, 106, 106, 106, 106, 71, 71, 45, 28, 28, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1388
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277463 none CCCCC(O)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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, 21, 20, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 30, 40, 106, 106, 106, 106, 106, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 30, 30, 106] 603
rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 343
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277463 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277463
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277463/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277463
Building REAL300025277464
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277464'
/scratch/stefan/7808390/working/building/REAL300025277464 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277464

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277464/0 /scratch/stefan/7808390/working/building/REAL300025277464 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/339
`/scratch/stefan/7808390/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)O)

`REAL300025277464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277464 none COC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 28, 28, 28, 28, 28, 28, 28, 24, 28, 17, 17, 12, 17, 7, 1, 1, 1, 1, 1, 1, 1, 29, 32, 32, 29, 29, 29, 29, 28, 28, 28, 28, 28, 28, 28, 28, 28, 24, 24, 17, 12, 12, 1, 32, 32, 32, 32, 96] 96
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])
total number of confs: 231
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277464 none COC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 17, 17, 28, 28, 28, 28, 28, 5, 9, 9, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 9, 17, 17, 28, 9, 9, 9, 9, 27] 96
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 35, 30, 31] set([0, 1, 2, 4, 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])
total number of confs: 149
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277464 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277464
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277464/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277464
Building REAL300025277465
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277465'
/scratch/stefan/7808390/working/building/REAL300025277465 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277465

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277465/0 /scratch/stefan/7808390/working/building/REAL300025277465 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/340
`/scratch/stefan/7808390/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSC1CC1)

`REAL300025277465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277465 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 116, 147, 179, 201, 201, 116, 116, 116, 83, 83, 62, 29, 29, 1, 116, 116, 116, 116, 116, 116, 147, 147, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277465 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 22, 39, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 2, 2, 5, 10, 24, 24, 2, 2, 2, 3, 3, 6, 22, 22, 116, 1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277465 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CSC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 47, 47, 47, 102, 135, 201, 201, 201, 201, 201, 24, 24, 24, 24, 21, 24, 5, 1, 1, 1, 1, 24, 24, 24, 35, 35, 47, 102, 102, 201, 24, 24, 24, 24, 24, 24, 21, 21, 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: 615
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277465 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277465
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277465/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277465
Building REAL300025277466
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277466'
/scratch/stefan/7808390/working/building/REAL300025277466 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277466

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277466/0 /scratch/stefan/7808390/working/building/REAL300025277466 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/341
`/scratch/stefan/7808390/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC1CCC1)

`REAL300025277466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277466 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 31, 31, 23, 31, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 123, 135, 144, 201, 201, 201, 67, 67, 67, 43, 43, 31, 23, 23, 1, 67, 67, 67, 67, 67, 67, 123, 123, 135, 135, 144, 144, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277466 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 14, 21, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 6, 8, 10, 27, 27, 27, 2, 2, 2, 3, 3, 6, 14, 14, 67, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 10, 10, 27, 27, 27, 27, 27, 27, 27] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277466 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 57, 57, 57, 97, 109, 201, 201, 201, 201, 201, 27, 27, 27, 27, 10, 27, 8, 6, 1, 1, 1, 1, 1, 27, 27, 27, 39, 39, 57, 97, 97, 201, 27, 27, 27, 27, 27, 27, 10, 10, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [54, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 617
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277466 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277466
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277466/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277466
Building REAL300025277467
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277467'
/scratch/stefan/7808390/working/building/REAL300025277467 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277467

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277467/0 /scratch/stefan/7808390/working/building/REAL300025277467 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/342
`/scratch/stefan/7808390/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277467 none CCC(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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, 178, 201, 117, 117, 117, 117, 117, 117, 117, 80, 117, 41, 41, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 178, 178, 117, 117, 117, 117, 117, 117, 117, 117, 117, 80, 80, 41, 25, 25, 1] 603
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])
total number of confs: 1512
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277467 none CCC(O)CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 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, 15, 7, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 28, 38, 117, 117, 117, 117, 117, 20, 20, 20, 20, 20, 15, 45, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 28, 28, 117] 603
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 366
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277467 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277467
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277467/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277467
Building REAL300025277468
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277468'
/scratch/stefan/7808390/working/building/REAL300025277468 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277468

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277468/0 /scratch/stefan/7808390/working/building/REAL300025277468 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/343
`/scratch/stefan/7808390/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277468 none CN1C(=O)CCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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: [6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 42, 48, 88, 88, 88, 88, 88, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 42, 42, 88] 96
rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277468 none CN1C(=O)CCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 5, 6, 6, 6, 6, 6, 6, 10, 28, 28, 28, 68, 73, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 28, 68, 68, 96] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277468 none CN1C(=O)CCC1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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, 88, 88, 88, 88, 88, 88, 88, 76, 88, 53, 53, 28, 53, 12, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 96, 88, 88, 88, 88, 88, 88, 88, 88, 88, 76, 76, 53, 28, 28, 1] 96
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 373
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277468 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277468
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277468/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277468
Building REAL300025277469
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277469'
/scratch/stefan/7808390/working/building/REAL300025277469 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277469

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277469/0 /scratch/stefan/7808390/working/building/REAL300025277469 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/344
`/scratch/stefan/7808390/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC=C1C#N)

`REAL300025277469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277469 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [145, 118, 78, 78, 34, 78, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 155, 155, 168, 168, 168, 168, 168, 168, 145, 145, 145, 118, 118, 78, 34, 34, 1, 145, 145, 145, 145, 145, 145, 168, 168] 168
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 621
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277469 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [1, 1, 1, 5, 16, 16, 16, 64, 80, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 2, 2, 2, 5, 5, 16, 64, 64, 145, 1, 1, 1, 1, 1, 1, 9, 9] 168
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
total number of confs: 378
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277469 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [9, 9, 9, 17, 44, 44, 44, 114, 130, 168, 168, 168, 168, 168, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 44, 114, 114, 168, 9, 9, 9, 9, 9, 9, 1, 1] 168
rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 535
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277469 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277469
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277469/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277469
Building REAL300025277470
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277470'
/scratch/stefan/7808390/working/building/REAL300025277470 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277470

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277470/0 /scratch/stefan/7808390/working/building/REAL300025277470 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/345
`/scratch/stefan/7808390/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277470 none CNC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 197, 201, 193, 142, 142, 142, 142, 142, 142, 142, 109, 142, 68, 68, 27, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 197, 193, 193, 142, 142, 142, 142, 142, 142, 142, 142, 142, 109, 109, 68, 27, 27, 1] 201
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])
total number of confs: 842
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277470 none CNC(=O)CCC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 24, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 37, 58, 142, 142, 142, 142, 142, 24, 24, 24, 24, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 37, 37, 142] 201
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 377
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277470 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277470
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277470/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277470
Building REAL300025277471
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277471'
/scratch/stefan/7808390/working/building/REAL300025277471 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277471

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277471/0 /scratch/stefan/7808390/working/building/REAL300025277471 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/346
`/scratch/stefan/7808390/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=CON=C1)

`REAL300025277471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277471 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=CON=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 37, 37, 25, 37, 12, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 126, 127, 201, 201, 201, 201, 82, 82, 82, 62, 62, 37, 25, 25, 1, 82, 82, 82, 82, 82, 82, 126, 126, 127, 127, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 687
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277471 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=CON=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 9, 9, 9, 27, 33, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 2, 2, 8, 10, 21, 21, 21, 21, 2, 2, 2, 4, 4, 9, 27, 27, 82, 1, 1, 1, 1, 1, 1, 8, 8, 10, 10, 21, 21] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277471 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1=CON=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 60, 60, 60, 114, 122, 201, 201, 201, 201, 201, 21, 21, 21, 20, 8, 20, 4, 1, 1, 1, 1, 1, 1, 21, 21, 21, 37, 37, 60, 114, 114, 201, 21, 21, 21, 21, 21, 21, 8, 8, 4, 4, 1, 1] 201
rigid atoms, others: [46, 47, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 658
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277471 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277471
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277471/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277471
Building REAL300025277472
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277472'
/scratch/stefan/7808390/working/building/REAL300025277472 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277472

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277472/0 /scratch/stefan/7808390/working/building/REAL300025277472 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/347
`/scratch/stefan/7808390/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSN=C1)

`REAL300025277472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277472 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 73, 51, 51, 26, 51, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 89, 89, 141, 201, 201, 201, 201, 88, 88, 88, 73, 73, 51, 26, 26, 1, 88, 88, 88, 88, 88, 88, 141, 141, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277472 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 35, 39, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 3, 3, 9, 17, 17, 17, 17, 2, 2, 2, 3, 3, 8, 35, 35, 88, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 252
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277472 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 31, 68, 68, 68, 148, 154, 201, 201, 201, 201, 201, 17, 17, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 68, 148, 148, 201, 17, 17, 17, 17, 17, 17, 5, 5, 1, 1] 201
rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 686
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277472 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277472
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277472/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277472
Building REAL300025277473
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277473'
/scratch/stefan/7808390/working/building/REAL300025277473 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277473

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277473/0 /scratch/stefan/7808390/working/building/REAL300025277473 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/348
`/scratch/stefan/7808390/working/3D/348' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C)

`REAL300025277473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277473 none C=CCC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 63, 51, 51, 51, 51, 51, 51, 51, 51, 48, 51, 27, 27, 22, 27, 11, 1, 1, 1, 1, 1, 1, 1, 51, 62, 62, 62, 66, 66, 66, 63, 63, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 48, 48, 27, 22, 22, 1, 62, 62, 62, 62, 62, 62] 66
rigid atoms, others: [48, 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, 49, 50, 51, 52, 53, 54])
total number of confs: 330
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: REAL300025277473 none C=CCC(C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 9, 6, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 21, 22, 51, 51, 51, 51, 51, 3, 6, 6, 6, 11, 11, 11, 7, 7, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 21, 21, 51, 6, 6, 6, 6, 6, 6] 66
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 186
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277473 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277473
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277473/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277473
Building REAL300025277474
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277474'
/scratch/stefan/7808390/working/building/REAL300025277474 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277474

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277474/0 /scratch/stefan/7808390/working/building/REAL300025277474 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/349
`/scratch/stefan/7808390/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCF)

`REAL300025277474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277474 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 37, 37, 25, 37, 12, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 178, 197, 201, 201, 97, 97, 97, 64, 64, 37, 25, 25, 1, 97, 97, 97, 97, 97, 97, 178, 178, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 941
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277474 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCCCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 7, 21, 27, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 2, 2, 8, 11, 12, 21, 2, 2, 2, 4, 4, 7, 21, 21, 97, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 21, 21] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 285
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277474 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277474
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277474/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277474
Building REAL300025277475
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277475'
/scratch/stefan/7808390/working/building/REAL300025277475 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277475

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277475/0 /scratch/stefan/7808390/working/building/REAL300025277475 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/350
`/scratch/stefan/7808390/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)C=CN1)

`REAL300025277475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277475 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 110, 56, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 153, 153, 201, 201, 201, 201, 201, 201, 143, 143, 143, 110, 110, 56, 30, 30, 1, 143, 143, 143, 143, 143, 143, 201, 201, 201, 201] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 717
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277475 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 41, 60, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 2, 2, 2, 5, 5, 12, 41, 41, 143, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45])
total number of confs: 326
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: REAL300025277475 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC(=O)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 45, 45, 106, 131, 201, 201, 201, 201, 201, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 45, 106, 106, 201, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 600
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277475 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277475
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277475/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277475
Building REAL300025277476
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277476'
/scratch/stefan/7808390/working/building/REAL300025277476 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277476

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277476/0 /scratch/stefan/7808390/working/building/REAL300025277476 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/351
`/scratch/stefan/7808390/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC([O-])=CS1)

`REAL300025277476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277476 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC([O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [132, 112, 85, 85, 37, 85, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 136, 136, 201, 201, 201, 201, 201, 132, 132, 132, 112, 112, 85, 37, 37, 1, 132, 132, 132, 132, 132, 132, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 614
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277476 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC([O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 7, 15, 15, 15, 48, 74, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 2, 2, 2, 7, 7, 15, 48, 48, 132, 1, 1, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42])
total number of confs: 338
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: REAL300025277476 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC([O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 22, 42, 42, 42, 109, 148, 201, 201, 201, 201, 201, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 42, 109, 109, 201, 9, 9, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 597
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277476 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277476
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277476/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277476
Building REAL300025277477
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277477'
/scratch/stefan/7808390/working/building/REAL300025277477 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277477

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277477/0 /scratch/stefan/7808390/working/building/REAL300025277477 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/352
`/scratch/stefan/7808390/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSN=C1)

`REAL300025277477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277477 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [83, 72, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 85, 85, 120, 120, 120, 120, 83, 83, 83, 72, 72, 53, 28, 28, 1, 83, 83, 83, 83, 83, 83, 120, 120] 120
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 386
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277477 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 14, 14, 14, 42, 48, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 2, 2, 2, 5, 5, 14, 42, 42, 83, 1, 1, 1, 1, 1, 1, 11, 11] 120
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41])
total number of confs: 245
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: REAL300025277477 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.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: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [11, 11, 11, 21, 45, 45, 45, 84, 92, 120, 120, 120, 120, 120, 11, 11, 11, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 11, 21, 21, 45, 84, 84, 120, 11, 11, 11, 11, 11, 11, 1, 1] 120
rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 384
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277477 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277477
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277477/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277477
Building REAL300025277478
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277478'
/scratch/stefan/7808390/working/building/REAL300025277478 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277478

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277478/0 /scratch/stefan/7808390/working/building/REAL300025277478 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/353
`/scratch/stefan/7808390/working/3D/353' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(N)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277478 none CN1N=C(N)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 35, 47, 138, 138, 138, 138, 138, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 35, 35, 138] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 294
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277478 none CN1N=C(N)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 9, 9, 9, 9, 9, 9, 20, 44, 44, 44, 104, 119, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 44, 104, 104, 201] 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, 46, 47])
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: REAL300025277478 none CN1N=C(N)C=C1C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 167, 138, 167, 138, 138, 138, 138, 102, 138, 53, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 138, 138, 138, 102, 102, 53, 29, 29, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 730
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277478 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277478
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277478/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277478
Building REAL300025277479
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277479'
/scratch/stefan/7808390/working/building/REAL300025277479 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277479

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277479/0 /scratch/stefan/7808390/working/building/REAL300025277479 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/354
`/scratch/stefan/7808390/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)C1)

`REAL300025277479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277479 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [116, 98, 69, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 118, 118, 148, 148, 148, 148, 148, 116, 116, 116, 98, 98, 69, 31, 31, 1, 116, 116, 116, 116, 116, 116, 148, 148, 148, 148, 148, 148, 148] 148
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277479 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 5, 15, 15, 15, 56, 66, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 2, 2, 2, 5, 5, 15, 56, 56, 116, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 148
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 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: REAL300025277479 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 16, 40, 40, 40, 98, 111, 148, 148, 148, 148, 148, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 40, 98, 98, 148, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 148
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 455
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277479 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277479
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277479/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277479
Building REAL300025277480
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277480'
/scratch/stefan/7808390/working/building/REAL300025277480 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277480

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277480/0 /scratch/stefan/7808390/working/building/REAL300025277480 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/355
`/scratch/stefan/7808390/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCSC1)

`REAL300025277480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277480 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 102, 59, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 149, 149, 201, 201, 201, 201, 201, 141, 141, 141, 102, 102, 59, 29, 29, 1, 141, 141, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 783
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277480 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 19, 19, 19, 53, 70, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 2, 2, 2, 7, 7, 19, 53, 53, 141, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 363
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277480 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 37, 37, 37, 96, 120, 201, 201, 201, 201, 201, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 37, 96, 96, 201, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 559
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277480 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277480
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277480/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277480
Building REAL300025277481
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277481'
/scratch/stefan/7808390/working/building/REAL300025277481 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277481

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277481/0 /scratch/stefan/7808390/working/building/REAL300025277481 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/356
`/scratch/stefan/7808390/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC(=O)N1)

`REAL300025277481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277481 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [88, 72, 50, 50, 23, 50, 11, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 107, 107, 107, 107, 107, 88, 88, 88, 72, 72, 50, 23, 23, 1, 88, 88, 88, 88, 88, 88, 107, 107, 107] 107
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 409
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277481 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 6, 15, 15, 15, 46, 51, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 15, 46, 46, 88, 1, 1, 1, 1, 1, 1, 8, 8, 8] 107
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 248
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277481 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)[C@H]1CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 18, 37, 37, 37, 79, 85, 107, 107, 107, 107, 107, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 37, 79, 79, 107, 8, 8, 8, 8, 8, 8, 1, 1, 1] 107
rigid atoms, others: [41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 350
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277481 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277481
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277481/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277481
Building REAL300025277482
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277482'
/scratch/stefan/7808390/working/building/REAL300025277482 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277482

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277482/0 /scratch/stefan/7808390/working/building/REAL300025277482 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/357
`/scratch/stefan/7808390/working/3D/357' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(N)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277482 none CN1C=C(N)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 38, 52, 145, 145, 145, 145, 145, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 38, 38, 145] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277482 none CN1C=C(N)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 11, 21, 46, 46, 46, 124, 143, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 46, 124, 124, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277482 none CN1C=C(N)C(C(=O)N2CCCC2(C)CNC(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 145, 177, 145, 145, 145, 145, 108, 145, 57, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 145, 145, 145, 145, 108, 108, 57, 29, 29, 1] 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])
total number of confs: 735
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277482 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277482
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277482/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277482
Building REAL300025277483
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277483'
/scratch/stefan/7808390/working/building/REAL300025277483 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277483

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277483/0 /scratch/stefan/7808390/working/building/REAL300025277483 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/358
`/scratch/stefan/7808390/working/3D/358' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C=C(C#N)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277483 none CC(C)C=C(C#N)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 138, 201, 201, 129, 138, 129, 129, 129, 129, 98, 129, 59, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 129, 129, 129, 129, 98, 98, 59, 30, 30, 1] 201
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 770
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277483 none CC(C)C=C(C#N)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 8, 3, 8, 8, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 27, 43, 129, 129, 129, 129, 129, 19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 27, 27, 129] 201
rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 319
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277483 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277483
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277483/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277483
Building REAL300025277484
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277484'
/scratch/stefan/7808390/working/building/REAL300025277484 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277484

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277484/0 /scratch/stefan/7808390/working/building/REAL300025277484 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/359
`/scratch/stefan/7808390/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NSC=C1N)

`REAL300025277484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277484 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NSC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [145, 121, 79, 79, 33, 79, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 154, 154, 169, 169, 169, 169, 169, 145, 145, 145, 121, 121, 79, 33, 33, 1, 145, 145, 145, 145, 145, 145, 169, 169, 169] 169
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 604
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277484 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NSC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 21, 21, 21, 69, 89, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 2, 2, 2, 7, 7, 21, 69, 69, 145, 1, 1, 1, 1, 1, 1, 11, 11, 11] 169
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025277484 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NSC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 23, 53, 53, 53, 113, 133, 169, 169, 169, 169, 169, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 23, 23, 53, 113, 113, 169, 11, 11, 11, 11, 11, 11, 1, 1, 1] 169
rigid atoms, others: [41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 539
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277484 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277484
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277484/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277484
Building REAL300025277485
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277485'
/scratch/stefan/7808390/working/building/REAL300025277485 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277485

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277485/0 /scratch/stefan/7808390/working/building/REAL300025277485 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/360
`/scratch/stefan/7808390/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC=N1)

`REAL300025277485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277485 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 129, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 156, 156, 195, 201, 201, 201, 201, 153, 153, 153, 129, 129, 61, 29, 29, 1, 153, 153, 153, 153, 153, 153, 195, 195, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277485 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 44, 67, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 2, 2, 8, 16, 16, 16, 16, 2, 2, 2, 5, 5, 12, 44, 44, 153, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277485 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 26, 43, 43, 43, 105, 130, 201, 201, 201, 201, 201, 16, 16, 16, 15, 9, 15, 1, 1, 1, 1, 1, 1, 16, 16, 16, 26, 26, 43, 105, 105, 201, 16, 16, 16, 16, 16, 16, 9, 9, 1, 1] 201
rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 613
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277485 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277485
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277485/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277485
Building REAL300025277486
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277486'
/scratch/stefan/7808390/working/building/REAL300025277486 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277486

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277486/0 /scratch/stefan/7808390/working/building/REAL300025277486 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/361
`/scratch/stefan/7808390/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C(=O)OC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277486 none CCC(C(=O)OC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [188, 174, 112, 174, 201, 201, 201, 107, 112, 107, 107, 107, 107, 82, 107, 56, 56, 28, 56, 12, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 174, 201, 201, 201, 107, 107, 107, 107, 107, 107, 107, 107, 107, 82, 82, 56, 28, 28, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 927
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277486 none CCC(C(=O)OC)C(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 6, 10, 10, 10, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 25, 36, 107, 107, 107, 107, 107, 8, 8, 8, 8, 8, 6, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 25, 25, 107] 201
rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 257
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277486 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277486
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277486/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277486
Building REAL300025277487
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277487'
/scratch/stefan/7808390/working/building/REAL300025277487 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277487

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277487/0 /scratch/stefan/7808390/working/building/REAL300025277487 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/362
`/scratch/stefan/7808390/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CSC1)

`REAL300025277487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277487 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [120, 102, 70, 70, 33, 70, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 120, 155, 155, 155, 120, 120, 120, 102, 102, 70, 33, 33, 1, 120, 120, 120, 120, 120, 120, 155, 155, 155, 155, 155] 155
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 589
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277487 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 15, 15, 15, 59, 70, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 15, 59, 59, 120, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 155
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277487 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CSC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 17, 38, 38, 38, 100, 115, 155, 155, 155, 155, 155, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 7, 7, 7, 17, 17, 38, 100, 100, 155, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 155
rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 487
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277487 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277487
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277487/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277487
Building REAL300025277488
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277488'
/scratch/stefan/7808390/working/building/REAL300025277488 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277488

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277488/0 /scratch/stefan/7808390/working/building/REAL300025277488 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/363
`/scratch/stefan/7808390/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)O1)

`REAL300025277488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277488 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [174, 132, 60, 60, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 199, 199, 201, 201, 201, 201, 201, 174, 174, 174, 132, 132, 60, 31, 31, 1, 174, 174, 174, 174, 174, 174, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 784
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277488 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
201  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, 18, 18, 18, 52, 74, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 2, 2, 2, 7, 7, 18, 52, 52, 174, 1, 1, 1, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025277488 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=C(N)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens 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, 25, 56, 56, 56, 125, 142, 201, 201, 201, 201, 201, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 25, 56, 125, 125, 201, 10, 10, 10, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277488 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277488
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277488/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277488
Building REAL300025277489
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277489'
/scratch/stefan/7808390/working/building/REAL300025277489 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277489

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277489/0 /scratch/stefan/7808390/working/building/REAL300025277489 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/364
`/scratch/stefan/7808390/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CC1)

`REAL300025277489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277489 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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: [143, 116, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 189, 201, 201, 201, 201, 143, 143, 143, 116, 116, 69, 30, 30, 1, 143, 143, 143, 143, 143, 143, 189, 189, 201, 201, 603, 201, 201, 201, 201] 603
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 1462
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277489 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
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, 4, 8, 8, 8, 32, 55, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 2, 2, 6, 10, 16, 10, 10, 2, 2, 2, 4, 4, 8, 32, 32, 143, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 48, 10, 10, 10, 10] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 394
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277489 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1(CO)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 18, 34, 34, 34, 94, 123, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 10, 1, 1, 1, 8, 1, 1, 10, 10, 10, 18, 18, 34, 94, 94, 201, 10, 10, 10, 10, 10, 10, 4, 4, 8, 8, 24, 1, 1, 1, 1] 603
rigid atoms, others: [46, 47, 48, 49, 20, 21, 22, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 626
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277489 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277489
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277489/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277489
Building REAL300025277490
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277490'
/scratch/stefan/7808390/working/building/REAL300025277490 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277490

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277490/0 /scratch/stefan/7808390/working/building/REAL300025277490 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/365
`/scratch/stefan/7808390/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=NC=CS1)

`REAL300025277490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277490 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=NC=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 80, 49, 49, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 110, 110, 168, 201, 201, 201, 201, 104, 104, 104, 80, 80, 49, 25, 25, 1, 104, 104, 104, 104, 104, 104, 168, 168, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 783
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277490 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=NC=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 8, 8, 8, 28, 39, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 2, 2, 10, 20, 20, 20, 20, 2, 2, 2, 3, 3, 8, 28, 28, 104, 1, 1, 1, 1, 1, 1, 10, 10, 20, 20] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277490 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=NC=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', '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, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 36, 52, 52, 52, 109, 122, 201, 201, 201, 201, 201, 20, 20, 20, 18, 4, 18, 1, 1, 1, 1, 1, 1, 21, 21, 21, 36, 36, 52, 109, 109, 201, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1] 201
rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277490 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277490
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277490/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277490
Building REAL300025277491
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277491'
/scratch/stefan/7808390/working/building/REAL300025277491 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277491

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277491/0 /scratch/stefan/7808390/working/building/REAL300025277491 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/366
`/scratch/stefan/7808390/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC=CO1)

`REAL300025277491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277491 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 125, 64, 64, 32, 64, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 166, 166, 201, 201, 201, 201, 201, 159, 159, 159, 125, 125, 64, 32, 32, 1, 159, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 793
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277491 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 14, 14, 14, 48, 71, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 2, 2, 2, 5, 5, 14, 48, 48, 159, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277491 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 23, 48, 48, 48, 116, 139, 201, 201, 201, 201, 201, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 48, 116, 116, 201, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/7808390/working/building/REAL300025277491 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277491
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277491/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277491
Building REAL300025277492
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277492'
/scratch/stefan/7808390/working/building/REAL300025277492 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277492

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277492/0 /scratch/stefan/7808390/working/building/REAL300025277492 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/367
`/scratch/stefan/7808390/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277492 none C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 76, 83, 56, 56, 32, 56, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 76, 76, 56, 32, 32, 1] 83
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])
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: REAL300025277492 none C=CC(=O)N1CCCC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 44, 52, 83, 83, 83, 83, 83, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 44, 44, 83] 83
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277492 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277492
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277492/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277492
Building REAL300025277493
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277493'
/scratch/stefan/7808390/working/building/REAL300025277493 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277493

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277493/0 /scratch/stefan/7808390/working/building/REAL300025277493 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/368
`/scratch/stefan/7808390/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC(N)=[NH2+])CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277493 none CC1(CNC(=O)CSC(N)=[NH2+])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.cat', 'N.pl3', 'N.pl3', 'H', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 6, 6, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 13, 14, 14, 14, 14, 15, 15, 15, 15, 15, 11, 11, 11, 11, 10, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 14, 14, 14, 15, 15, 11, 11, 11, 11, 11, 11, 10, 10, 1] 15
rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 43
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277493 none CC1(CNC(=O)CSC(N)=[NH2+])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.cat', 'N.pl3', 'N.pl3', 'H', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 6, 6, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
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, 3, 7, 7, 7, 10, 13, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 5, 6, 11, 11, 11, 11, 11, 2, 2, 2, 3, 3, 7, 10, 10, 14, 14, 1, 1, 1, 1, 1, 1, 5, 5, 11] 15
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 80
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277493 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277493
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277493/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277493
Building REAL300025277494
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277494'
/scratch/stefan/7808390/working/building/REAL300025277494 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277494

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277494/0 /scratch/stefan/7808390/working/building/REAL300025277494 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/369
`/scratch/stefan/7808390/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCC[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277494 none CC1(CNC(=O)CCC[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 32, 49, 49, 49, 156, 164, 201, 201, 201, 22, 22, 22, 22, 18, 22, 13, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 32, 32, 49, 156, 156, 184, 184, 198, 197, 22, 22, 22, 22, 22, 22, 18, 18, 1] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 961
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277494 none CC1(CNC(=O)CCC[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 3, 6, 6, 6, 40, 51, 77, 117, 117, 1, 1, 1, 1, 1, 2, 2, 5, 8, 22, 22, 22, 22, 22, 2, 2, 2, 3, 3, 6, 40, 40, 61, 61, 74, 73, 1, 1, 1, 1, 1, 1, 5, 5, 22] 201
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 561
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277494 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277494
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277494/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277494
Building REAL300025277495
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277495'
/scratch/stefan/7808390/working/building/REAL300025277495 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277495

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277495/0 /scratch/stefan/7808390/working/building/REAL300025277495 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/370
`/scratch/stefan/7808390/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277495 none CC(CF)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 141, 201, 201, 141, 141, 77, 46, 46, 46, 46, 46, 46, 46, 34, 46, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 141, 77, 77, 46, 46, 46, 46, 46, 46, 46, 46, 46, 34, 34, 1] 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])
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: REAL300025277495 none CC(CF)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [53, 15, 53, 57, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 53, 53, 53, 53, 57, 57, 15, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 46] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/7808390/working/building/REAL300025277495 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277495
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277495/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277495
Building REAL300025277496
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277496'
/scratch/stefan/7808390/working/building/REAL300025277496 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277496

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277496/0 /scratch/stefan/7808390/working/building/REAL300025277496 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/371
`/scratch/stefan/7808390/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C[C@@H]2COC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277496 none CC1(CNC(=O)C[C@@H]2COC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [76, 56, 31, 31, 8, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 81, 81, 132, 147, 201, 201, 201, 201, 201, 76, 76, 76, 56, 56, 31, 8, 8, 1, 1, 1, 1, 3, 76, 76, 76, 76, 76, 76, 132, 132, 201] 603
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 695
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: REAL300025277496 none CC1(CNC(=O)C[C@@H]2COC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 8, 8, 8, 40, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 4, 4, 8, 15, 52, 52, 52, 52, 52, 2, 2, 2, 3, 3, 8, 40, 40, 76, 76, 76, 76, 228, 1, 1, 1, 1, 1, 1, 8, 8, 52] 603
rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 573
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: REAL300025277496 none CC1(CNC(=O)C[C@@H]2COC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [52, 52, 52, 65, 88, 88, 88, 174, 201, 201, 201, 201, 201, 201, 201, 52, 52, 52, 49, 35, 49, 12, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 65, 65, 88, 174, 174, 201, 201, 201, 201, 603, 52, 52, 52, 52, 52, 52, 35, 35, 1] 603
rigid atoms, others: [50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 1418
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277496 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277496
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277496/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277496
Building REAL300025277497
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277497'
/scratch/stefan/7808390/working/building/REAL300025277497 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277497

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277497/0 /scratch/stefan/7808390/working/building/REAL300025277497 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/372
`/scratch/stefan/7808390/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C=CC2=NC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277497 none CC1(CNC(=O)C=CC2=NC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 42, 25, 25, 7, 25, 7, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 94, 119, 201, 201, 201, 201, 201, 57, 57, 57, 42, 42, 25, 7, 7, 1, 1, 57, 57, 57, 57, 57, 57, 94, 94, 201] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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])
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: REAL300025277497 none CC1(CNC(=O)C=CC2=NC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 7, 7, 7, 31, 31, 57, 57, 57, 57, 1, 1, 1, 1, 1, 2, 2, 6, 11, 52, 52, 52, 52, 52, 2, 2, 2, 4, 4, 7, 31, 31, 57, 57, 1, 1, 1, 1, 1, 1, 6, 6, 52] 201
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277497 none CC1(CNC(=O)C=CC2=NC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [52, 52, 52, 79, 93, 93, 93, 138, 138, 201, 201, 201, 201, 52, 52, 52, 52, 39, 52, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 79, 79, 93, 138, 138, 201, 201, 52, 52, 52, 52, 52, 52, 39, 39, 1] 201
rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 668
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277497 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277497
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277497/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277497
Building REAL300025277498
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277498'
/scratch/stefan/7808390/working/building/REAL300025277498 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277498

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277498/0 /scratch/stefan/7808390/working/building/REAL300025277498 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/373
`/scratch/stefan/7808390/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277498 none CC(CC1CCC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 5, 23, 45, 63, 63, 63, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 37, 37, 37, 37, 37, 23, 23, 23, 23, 45, 45, 63, 63, 63, 63, 63, 63, 63, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 37] 201
rigid atoms, others: [48, 17, 10, 11, 12, 13, 14, 47, 16, 49, 50, 51, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54])
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: REAL300025277498 none CC(CC1CCC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 12, 32, 32, 32, 46, 63, 63, 63, 63, 63, 63, 63, 63, 90, 124, 201, 201, 201, 201, 201, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 32, 46, 46, 63, 63, 63, 63, 63, 63, 63, 63, 63, 90, 90, 201] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 39, 34, 35, 36, 38, 37] set([0, 1, 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, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
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: REAL300025277498 none CC(CC1CCC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 165, 185, 201, 201, 201, 77, 77, 56, 37, 37, 37, 37, 37, 37, 37, 26, 37, 13, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 185, 185, 201, 201, 201, 201, 201, 201, 201, 77, 56, 56, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 26, 1] 201
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 889
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277498 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277498
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277498/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277498
Building REAL300025277499
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277499'
/scratch/stefan/7808390/working/building/REAL300025277499 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277499

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277499/0 /scratch/stefan/7808390/working/building/REAL300025277499 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/374
`/scratch/stefan/7808390/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277499 none CC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 40, 40, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 99, 99, 99, 99, 99, 40, 40, 40, 40, 40, 40, 40, 40, 17, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 99, 40, 40] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49])
total number of confs: 242
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277499 none CC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 24, 40, 40, 40, 40, 40, 40, 48, 48, 95, 135, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 10, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 95, 95, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277499 none CC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 182, 99, 99, 99, 99, 99, 99, 80, 33, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 99, 99, 99, 99, 99, 99, 99, 99, 99, 33, 33, 1, 201, 201] 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])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277499 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277499
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277499/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277499
Building REAL300025277500
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277500'
/scratch/stefan/7808390/working/building/REAL300025277500 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277500

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277500/0 /scratch/stefan/7808390/working/building/REAL300025277500 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/375
`/scratch/stefan/7808390/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277500 none CC1(CNC(=O)CCC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [90, 63, 42, 42, 15, 42, 7, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 129, 146, 201, 201, 201, 201, 201, 90, 90, 90, 63, 63, 42, 15, 15, 7, 7, 1, 1, 1, 90, 90, 90, 90, 90, 90, 129, 129, 201] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 704
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277500 none CC1(CNC(=O)CCC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 6, 6, 6, 34, 54, 90, 90, 90, 90, 1, 1, 1, 1, 1, 2, 2, 6, 12, 43, 43, 43, 43, 43, 2, 2, 2, 3, 3, 6, 34, 34, 54, 54, 90, 90, 90, 1, 1, 1, 1, 1, 1, 6, 6, 43] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277500 none CC1(CNC(=O)CCC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [42, 42, 42, 56, 69, 69, 69, 171, 188, 201, 201, 201, 201, 42, 42, 42, 42, 32, 42, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 56, 56, 69, 171, 171, 188, 188, 201, 201, 201, 42, 42, 42, 42, 42, 42, 32, 32, 1] 201
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 819
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277500 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277500
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277500/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277500
Building REAL300025277501
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277501'
/scratch/stefan/7808390/working/building/REAL300025277501 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277501

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277501/0 /scratch/stefan/7808390/working/building/REAL300025277501 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/376
`/scratch/stefan/7808390/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(O)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277501 none CC1(C)CC(O)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [36, 36, 36, 36, 10, 36, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 19, 76, 76, 76, 76, 76, 36, 36, 36, 36, 36, 36, 36, 36, 36, 108, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 76, 36, 36] 603
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 16, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52])
total number of confs: 333
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: REAL300025277501 none CC1(C)CC(O)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 9, 9, 9, 24, 36, 36, 36, 36, 36, 36, 41, 41, 84, 135, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 3, 9, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 36, 84, 84, 201, 1, 1] 603
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 51, 52, 26] set([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, 35, 36, 37, 38, 39, 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: REAL300025277501 none CC1(C)CC(O)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 154, 201, 154, 154, 123, 76, 76, 76, 76, 76, 76, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 154, 123, 123, 76, 76, 76, 76, 76, 76, 76, 76, 76, 30, 30, 1, 201, 201] 603
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])
total number of confs: 1371
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277501 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277501
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277501/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277501
Building REAL300025277502
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277502'
/scratch/stefan/7808390/working/building/REAL300025277502 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277502

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277502/0 /scratch/stefan/7808390/working/building/REAL300025277502 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/377
`/scratch/stefan/7808390/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CC2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277502 none CC1(CNC(=O)CC2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 22, 22, 6, 22, 1, 1, 1, 7, 7, 1, 1, 56, 56, 56, 56, 56, 56, 56, 91, 107, 189, 189, 189, 189, 189, 56, 56, 56, 39, 39, 22, 6, 6, 7, 7, 7, 7, 7, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 91, 91, 189] 201
rigid atoms, others: [43, 6, 7, 8, 41, 42, 11, 12, 40] set([0, 1, 2, 3, 4, 5, 9, 10, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 573
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.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: REAL300025277502 none CC1(CNC(=O)CC2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 80, 80, 80, 162, 189, 201, 201, 189, 189, 39, 39, 39, 39, 31, 39, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 56, 56, 80, 162, 162, 201, 201, 201, 201, 201, 189, 189, 189, 189, 39, 39, 39, 39, 39, 39, 31, 31, 1] 201
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 841
number of broken/clashed sets: 16
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277502 none CC1(CNC(=O)CC2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 32, 56, 83, 83, 56, 56, 1, 1, 1, 1, 1, 2, 2, 5, 11, 39, 39, 39, 39, 39, 2, 2, 2, 3, 3, 6, 32, 32, 83, 83, 83, 83, 83, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 5, 5, 39] 201
rigid atoms, others: [0, 1, 2, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 50, 51, 52])
total number of confs: 358
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277502 none CC1(CNC(=O)CC2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 41, 41, 14, 41, 7, 1, 1, 1, 1, 7, 7, 83, 83, 83, 83, 83, 83, 83, 113, 128, 201, 201, 201, 201, 201, 83, 83, 83, 64, 64, 41, 14, 14, 1, 1, 1, 1, 1, 7, 7, 7, 7, 83, 83, 83, 83, 83, 83, 113, 113, 201] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 641
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277502 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277502
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277502/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277502
Building REAL300025277503
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277503'
/scratch/stefan/7808390/working/building/REAL300025277503 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277503

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277503/0 /scratch/stefan/7808390/working/building/REAL300025277503 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/378
`/scratch/stefan/7808390/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)[C@@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277503 none CC1(CNC(=O)[C@@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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: [67, 47, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 83, 128, 201, 201, 201, 201, 201, 67, 67, 67, 47, 47, 10, 1, 1, 67, 67, 67, 67, 67, 67, 83, 83, 201] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 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: REAL300025277503 none CC1(CNC(=O)[C@@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 6, 18, 18, 18, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 2, 2, 5, 9, 40, 40, 40, 40, 40, 2, 2, 2, 6, 6, 18, 67, 67, 1, 1, 1, 1, 1, 1, 5, 5, 40] 201
rigid atoms, others: [0, 1, 2, 34, 36, 37, 38, 39, 12, 13, 14, 15, 16, 35] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277503 none CC1(CNC(=O)[C@@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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: [40, 40, 40, 79, 125, 125, 125, 201, 201, 201, 201, 201, 40, 40, 40, 40, 33, 40, 12, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 79, 79, 125, 201, 201, 40, 40, 40, 40, 40, 40, 33, 33, 1] 201
rigid atoms, others: [42, 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])
total number of confs: 719
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277503 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277503
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277503/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277503
Building REAL300025277504
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277504'
/scratch/stefan/7808390/working/building/REAL300025277504 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277504

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277504/0 /scratch/stefan/7808390/working/building/REAL300025277504 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/379
`/scratch/stefan/7808390/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2C3C4CC2CC43)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277504 none CC1(CNC(=O)C2C3C4CC2CC43)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [20, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 21, 21, 52, 74, 109, 109, 109, 109, 109, 20, 20, 20, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 52, 52, 109] 109
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 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])
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: REAL300025277504 none CC1(CNC(=O)C2C3C4CC2CC43)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 8, 8, 8, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 3, 3, 10, 17, 53, 53, 53, 53, 53, 2, 2, 2, 5, 5, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 10, 10, 53] 109
rigid atoms, others: [0, 1, 2, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277504 none CC1(CNC(=O)C2C3C4CC2CC43)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 81, 87, 87, 87, 109, 109, 109, 109, 109, 109, 53, 53, 53, 51, 35, 51, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 81, 81, 87, 109, 109, 109, 109, 109, 109, 109, 109, 109, 53, 53, 53, 53, 53, 53, 35, 35, 1] 109
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 433
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277504 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277504
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277504/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277504
Building REAL300025277505
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277505'
/scratch/stefan/7808390/working/building/REAL300025277505 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277505

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277505/0 /scratch/stefan/7808390/working/building/REAL300025277505 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/380
`/scratch/stefan/7808390/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)[C@@H](O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277505 none CC1(CNC(=O)[C@@H](O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [39, 29, 15, 15, 5, 15, 1, 5, 5, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 40, 40, 58, 61, 70, 70, 70, 70, 70, 39, 39, 39, 29, 29, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 58, 58, 70] 210
rigid atoms, others: [35, 36, 37, 6, 39, 40, 9, 10, 11, 12, 13, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 296
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277505 none CC1(CNC(=O)[C@@H](O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 27, 27, 27, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 6, 8, 22, 22, 22, 22, 22, 2, 2, 2, 3, 3, 7, 81, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 6, 6, 22] 210
rigid atoms, others: [0, 1, 2, 49, 48, 44, 45, 14, 15, 16, 17, 18, 46, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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, 50, 51, 52])
total number of confs: 271
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277505 none CC1(CNC(=O)[C@@H](O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 24, 38, 38, 38, 64, 64, 64, 70, 70, 70, 70, 22, 22, 22, 22, 18, 22, 13, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 24, 24, 38, 192, 70, 70, 70, 70, 70, 70, 70, 70, 70, 22, 22, 22, 22, 22, 22, 18, 18, 1] 210
rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 460
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277505 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277505
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277505/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277505
Building REAL300025277506
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277506'
/scratch/stefan/7808390/working/building/REAL300025277506 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277506

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277506/0 /scratch/stefan/7808390/working/building/REAL300025277506 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/381
`/scratch/stefan/7808390/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277506 none CC(=O)NCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 169, 102, 102, 102, 79, 45, 45, 45, 45, 45, 45, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 196, 196, 169, 169, 102, 79, 79, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 29, 1] 201
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])
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: REAL300025277506 none CC(=O)NCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 30, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 45, 45, 45, 45, 45, 54, 54, 54, 54, 43, 43, 30, 30, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 45] 201
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277506 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277506
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277506/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277506
Building REAL300025277507
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277507'
/scratch/stefan/7808390/working/building/REAL300025277507 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277507

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277507/0 /scratch/stefan/7808390/working/building/REAL300025277507 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/382
`/scratch/stefan/7808390/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277507 none CC1(CNC(=O)C2=CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [16, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 18, 18, 35, 46, 65, 65, 65, 65, 65, 16, 16, 16, 12, 12, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 35, 35, 65] 65
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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])
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: REAL300025277507 none CC1(CNC(=O)C2=CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 4, 4, 8, 14, 34, 34, 34, 34, 34, 2, 2, 2, 4, 4, 6, 16, 16, 16, 1, 1, 1, 1, 1, 1, 8, 8, 34] 65
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277507 none CC1(CNC(=O)C2=CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 50, 51, 51, 51, 65, 65, 65, 65, 65, 34, 34, 34, 32, 25, 32, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 50, 50, 51, 65, 65, 65, 34, 34, 34, 34, 34, 34, 25, 25, 1] 65
rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 221
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277507 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277507
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277507/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277507
Building REAL300025277508
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277508'
/scratch/stefan/7808390/working/building/REAL300025277508 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277508

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277508/0 /scratch/stefan/7808390/working/building/REAL300025277508 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/383
`/scratch/stefan/7808390/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277508 none CC1CCCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 30, 110, 110, 110, 110, 110, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 15, 15, 110] 201
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 247
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: REAL300025277508 none CC1CCCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 10, 19, 19, 19, 19, 19, 19, 28, 28, 70, 113, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 70, 70, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 513
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: REAL300025277508 none CC1CCCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 168, 110, 110, 110, 110, 110, 110, 84, 32, 84, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 168, 168, 110, 110, 110, 110, 110, 110, 110, 110, 110, 32, 32, 1] 201
rigid atoms, others: [51, 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, 50])
total number of confs: 681
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277508 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277508
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277508/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277508
Building REAL300025277509
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277509'
/scratch/stefan/7808390/working/building/REAL300025277509 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277509

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277509/0 /scratch/stefan/7808390/working/building/REAL300025277509 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/384
`/scratch/stefan/7808390/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277509 none CC1CCC(C)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 26, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 18, 77, 77, 77, 77, 77, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 77, 26, 26] 201
rigid atoms, others: [16, 45, 9, 10, 11, 12, 13, 14, 15, 48, 49, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52, 53, 54])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277509 none CC1CCC(C)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 18, 26, 26, 26, 26, 26, 26, 34, 34, 70, 113, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 5, 18, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 70, 70, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 53, 54, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277509 none CC1CCC(C)(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 146, 201, 146, 146, 117, 77, 77, 77, 77, 77, 77, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 117, 117, 77, 77, 77, 77, 77, 77, 77, 77, 77, 30, 30, 1, 201, 201] 201
rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] 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, 50, 51, 53, 54])
total number of confs: 738
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277509 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277509
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277509/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277509
Building REAL300025277510
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277510'
/scratch/stefan/7808390/working/building/REAL300025277510 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277510

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277510/0 /scratch/stefan/7808390/working/building/REAL300025277510 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/385
`/scratch/stefan/7808390/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277510 none C=C(C)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 123, 123, 123, 97, 63, 63, 63, 63, 63, 63, 60, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 123, 97, 97, 63, 63, 63, 63, 63, 63, 63, 63, 63, 31, 31, 1] 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])
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: REAL300025277510 none C=C(C)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 41, 58, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 63, 63, 63, 63, 63, 58, 58, 58, 58, 58, 41, 41, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 63] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277510 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277510
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277510/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277510
Building REAL300025277511
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277511'
/scratch/stefan/7808390/working/building/REAL300025277511 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277511

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277511/0 /scratch/stefan/7808390/working/building/REAL300025277511 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/386
`/scratch/stefan/7808390/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CCC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025277511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277511 none CC1=CCC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 59, 59, 59, 59, 59, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 59, 38, 38, 38, 38] 201
rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 194
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277511 none CC1=CCC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 28, 38, 38, 38, 38, 38, 38, 42, 42, 76, 116, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 28, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38, 76, 76, 201, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 49, 50, 51, 52, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 549
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: REAL300025277511 none CC1=CCC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 119, 119, 119, 95, 59, 59, 59, 59, 59, 59, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 95, 95, 59, 59, 59, 59, 59, 59, 59, 59, 59, 31, 31, 1, 201, 201, 201, 201] 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: 732
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277511 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277511
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277511/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277511
Building REAL300025277512
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277512'
/scratch/stefan/7808390/working/building/REAL300025277512 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277512

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277512/0 /scratch/stefan/7808390/working/building/REAL300025277512 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/387
`/scratch/stefan/7808390/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277512 none CCSCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 194, 125, 125, 125, 88, 49, 49, 49, 49, 49, 49, 49, 31, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 125, 88, 88, 49, 49, 49, 49, 49, 49, 49, 49, 49, 31, 31, 1] 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])
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: REAL300025277512 none CCSCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [54, 41, 29, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 49, 49, 49, 49, 49, 54, 54, 54, 54, 54, 29, 29, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 49] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277512 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277512
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277512/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277512
Building REAL300025277513
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277513'
/scratch/stefan/7808390/working/building/REAL300025277513 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277513

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277513/0 /scratch/stefan/7808390/working/building/REAL300025277513 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/388
`/scratch/stefan/7808390/working/3D/388' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277513 none CC(C)=C(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 201, 165, 165, 126, 86, 86, 86, 86, 86, 86, 67, 33, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 126, 126, 86, 86, 86, 86, 86, 86, 86, 86, 86, 33, 33, 1] 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])
total number of confs: 753
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277513 none CC(C)=C(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 30, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 86, 86, 86, 86, 86, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 86] 201
rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 234
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277513 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277513
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277513/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277513
Building REAL300025277514
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277514'
/scratch/stefan/7808390/working/building/REAL300025277514 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277514

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277514/0 /scratch/stefan/7808390/working/building/REAL300025277514 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/389
`/scratch/stefan/7808390/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C(F)(F)C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277514 none CC1(CNC(=O)C(F)(F)C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 15, 15, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [39, 39, 39, 67, 128, 128, 128, 201, 201, 201, 201, 201, 39, 39, 39, 39, 31, 39, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 67, 67, 128, 201, 39, 39, 39, 39, 39, 39, 31, 31, 1] 201
rigid atoms, others: [41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025277514 none CC1(CNC(=O)C(F)(F)C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 5, 15, 15, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 14, 14, 14, 51, 51, 51, 56, 56, 1, 1, 1, 1, 1, 2, 2, 4, 7, 39, 39, 39, 39, 39, 2, 2, 2, 4, 4, 14, 56, 1, 1, 1, 1, 1, 1, 4, 4, 39] 201
rigid atoms, others: [0, 1, 2, 34, 36, 37, 38, 33, 12, 13, 14, 15, 16, 35] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277514 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277514
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277514/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277514
Building REAL300025277515
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277515'
/scratch/stefan/7808390/working/building/REAL300025277515 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277515

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277515/0 /scratch/stefan/7808390/working/building/REAL300025277515 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/390
`/scratch/stefan/7808390/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277515 none CCCC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 164, 131, 164, 131, 131, 86, 47, 47, 47, 47, 47, 47, 47, 31, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 164, 492, 131, 86, 86, 47, 47, 47, 47, 47, 47, 47, 47, 47, 31, 31, 1] 603
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])
total number of confs: 1406
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277515 none CCCC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [44, 42, 23, 10, 23, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 47, 47, 47, 47, 47, 44, 44, 44, 44, 44, 44, 44, 23, 69, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 47] 603
rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277515 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277515
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277515/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277515
Building REAL300025277516
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277516'
/scratch/stefan/7808390/working/building/REAL300025277516 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277516

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277516/0 /scratch/stefan/7808390/working/building/REAL300025277516 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/391
`/scratch/stefan/7808390/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277516 none CCCCC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 164, 129, 164, 129, 129, 75, 44, 44, 44, 44, 44, 44, 44, 30, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 492, 129, 75, 75, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 30, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1399
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277516 none CCCCC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [41, 43, 41, 20, 10, 20, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 44, 44, 44, 44, 44, 43, 43, 43, 43, 43, 43, 43, 43, 43, 20, 60, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 44] 603
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 337
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277516 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277516
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277516/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277516
Building REAL300025277517
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277517'
/scratch/stefan/7808390/working/building/REAL300025277517 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277517

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277517/0 /scratch/stefan/7808390/working/building/REAL300025277517 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/392
`/scratch/stefan/7808390/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)O)

`REAL300025277517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277517 none COC(C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 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: [187, 187, 146, 146, 146, 96, 55, 55, 55, 55, 55, 55, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 187, 201, 201, 187, 187, 187, 187, 146, 96, 96, 55, 55, 55, 55, 55, 55, 55, 55, 55, 31, 31, 1, 201, 201, 201, 201, 603] 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])
total number of confs: 1502
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277517 none COC(C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 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: [31, 26, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 55, 55, 55, 55, 55, 26, 43, 43, 31, 31, 31, 26, 10, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 55, 43, 43, 43, 43, 129] 603
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 396
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277517 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277517
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277517/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277517
Building REAL300025277518
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277518'
/scratch/stefan/7808390/working/building/REAL300025277518 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277518

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277518/0 /scratch/stefan/7808390/working/building/REAL300025277518 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/393
`/scratch/stefan/7808390/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277518 none CC1(CNC(=O)CSC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [142, 119, 75, 75, 29, 75, 6, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142, 177, 180, 201, 201, 201, 201, 201, 142, 142, 142, 119, 119, 75, 29, 29, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 177, 177, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 801
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277518 none CC1(CNC(=O)CSC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 7, 7, 7, 32, 94, 142, 142, 1, 1, 1, 1, 1, 2, 2, 5, 6, 22, 22, 22, 22, 22, 2, 2, 2, 3, 3, 7, 32, 32, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 5, 5, 22] 201
rigid atoms, others: [0, 1, 2, 43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
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: REAL300025277518 none CC1(CNC(=O)CSC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 14, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [22, 22, 22, 29, 50, 50, 50, 115, 177, 201, 201, 22, 22, 22, 22, 15, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 29, 29, 50, 115, 115, 201, 201, 201, 201, 201, 22, 22, 22, 22, 22, 22, 15, 15, 1] 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])
total number of confs: 663
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277518 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277518
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277518/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277518
Building REAL300025277519
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277519'
/scratch/stefan/7808390/working/building/REAL300025277519 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277519

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277519/0 /scratch/stefan/7808390/working/building/REAL300025277519 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/394
`/scratch/stefan/7808390/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277519 none CC1(CNC(=O)CCCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 74, 47, 47, 13, 47, 7, 6, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 127, 129, 201, 201, 201, 201, 201, 101, 101, 101, 74, 74, 47, 13, 13, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 127, 127, 201] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 45, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 703
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277519 none CC1(CNC(=O)CCCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 34, 46, 66, 101, 101, 101, 1, 1, 1, 1, 1, 2, 2, 4, 6, 23, 23, 23, 23, 23, 2, 2, 2, 3, 3, 6, 34, 34, 55, 55, 64, 65, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 4, 4, 23] 201
rigid atoms, others: [0, 1, 2, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 52, 53, 54])
total number of confs: 521
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277519 none CC1(CNC(=O)CCCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 37, 37, 37, 120, 130, 153, 201, 201, 201, 23, 23, 23, 23, 20, 23, 13, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 28, 28, 37, 120, 120, 145, 145, 152, 152, 201, 201, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 23, 20, 20, 1] 201
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 925
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277519 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277519
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277519/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277519
Building REAL300025277520
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277520'
/scratch/stefan/7808390/working/building/REAL300025277520 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277520

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277520/0 /scratch/stefan/7808390/working/building/REAL300025277520 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/395
`/scratch/stefan/7808390/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277520 none CCC(O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 184, 201, 104, 104, 104, 82, 48, 48, 48, 48, 48, 48, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 184, 184, 104, 82, 82, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 1] 603
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])
total number of confs: 1489
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277520 none CCC(O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [56, 51, 35, 51, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 48, 48, 48, 48, 48, 56, 56, 56, 56, 56, 51, 153, 35, 35, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 48] 603
rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 479
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277520 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277520
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277520/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277520
Building REAL300025277521
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277521'
/scratch/stefan/7808390/working/building/REAL300025277521 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277521

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277521/0 /scratch/stefan/7808390/working/building/REAL300025277521 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/396
`/scratch/stefan/7808390/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(Cl)=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277521 none CC(Cl)=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 157, 157, 157, 119, 78, 78, 78, 78, 78, 78, 68, 31, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 157, 119, 119, 78, 78, 78, 78, 78, 78, 78, 78, 78, 31, 31, 1] 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])
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: REAL300025277521 none CC(Cl)=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [36, 36, 36, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 78, 78, 78, 78, 78, 36, 36, 36, 36, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 78] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277521 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277521
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277521/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277521
Building REAL300025277522
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277522'
/scratch/stefan/7808390/working/building/REAL300025277522 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277522

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277522/0 /scratch/stefan/7808390/working/building/REAL300025277522 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/397
`/scratch/stefan/7808390/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277522 none CC=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 154, 154, 154, 146, 98, 98, 98, 98, 98, 98, 89, 33, 89, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 154, 146, 146, 98, 98, 98, 98, 98, 98, 98, 98, 98, 33, 33, 1] 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])
total number of confs: 774
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277522 none CC=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [40, 40, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 19, 98, 98, 98, 98, 98, 40, 40, 40, 40, 40, 10, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 98] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 39, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 258
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277522 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277522
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277522/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277522
Building REAL300025277523
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277523'
/scratch/stefan/7808390/working/building/REAL300025277523 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277523

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277523/0 /scratch/stefan/7808390/working/building/REAL300025277523 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/398
`/scratch/stefan/7808390/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)NCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277523 none CN1C(=O)NCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [41, 41, 41, 41, 41, 41, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 22, 81, 81, 81, 81, 81, 41, 41, 41, 41, 41, 41, 41, 18, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 12, 81] 201
rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277523 none CN1C(=O)NCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 22, 41, 41, 41, 41, 41, 41, 48, 48, 85, 125, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 7, 22, 22, 41, 41, 41, 41, 41, 41, 41, 41, 41, 85, 85, 201] 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: 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: REAL300025277523 none CN1C(=O)NCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 183, 183, 183, 138, 81, 81, 81, 81, 81, 81, 74, 31, 74, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 183, 138, 138, 81, 81, 81, 81, 81, 81, 81, 81, 81, 31, 31, 1] 201
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/7808390/working/building/REAL300025277523 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277523
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277523/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277523
Building REAL300025277524
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277524'
/scratch/stefan/7808390/working/building/REAL300025277524 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277524

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277524/0 /scratch/stefan/7808390/working/building/REAL300025277524 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/399
`/scratch/stefan/7808390/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)(F)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277524 none CCC(F)(F)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 201, 201, 133, 133, 86, 49, 49, 49, 49, 49, 49, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 133, 86, 86, 49, 49, 49, 49, 49, 49, 49, 49, 49, 30, 30, 1] 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])
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: REAL300025277524 none CCC(F)(F)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 15, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [52, 42, 10, 42, 42, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 49, 49, 49, 49, 49, 54, 54, 54, 54, 54, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 49] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 310
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277524 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277524
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277524/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277524
Building REAL300025277525
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277525'
/scratch/stefan/7808390/working/building/REAL300025277525 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277525

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277525/0 /scratch/stefan/7808390/working/building/REAL300025277525 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/400
`/scratch/stefan/7808390/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CCCCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277525 none CC1(CNC(=O)C2CCCCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [27, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 28, 28, 48, 61, 89, 89, 89, 89, 89, 27, 27, 27, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 48, 48, 89] 89
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 274
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277525 none CC1(CNC(=O)C2CCCCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 8, 14, 42, 42, 42, 42, 42, 2, 2, 2, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 8, 8, 42] 89
rigid atoms, others: [0, 1, 2, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 49, 50, 51])
total number of confs: 155
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: REAL300025277525 none CC1(CNC(=O)C2CCCCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 63, 71, 71, 71, 89, 89, 89, 89, 89, 89, 42, 42, 42, 41, 28, 41, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 63, 63, 71, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 42, 42, 42, 42, 42, 42, 28, 28, 1] 89
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 358
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277525 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277525
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277525/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277525
Building REAL300025277526
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277526'
/scratch/stefan/7808390/working/building/REAL300025277526 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277526

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277526/0 /scratch/stefan/7808390/working/building/REAL300025277526 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/401
`/scratch/stefan/7808390/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1F)

`REAL300025277526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277526 none CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 59, 59, 59, 59, 59, 43, 43, 43, 43, 43, 43, 22, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 59, 43, 43, 43] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 39, 38, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45])
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: REAL300025277526 none CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 5, 5, 26, 43, 43, 43, 43, 43, 43, 45, 45, 66, 105, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 5, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43, 66, 66, 201, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 43, 44, 45, 22, 23, 24] set([3, 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, 38, 39, 40, 41, 42])
total number of confs: 488
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277526 none CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 128, 59, 59, 59, 59, 59, 59, 59, 42, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 160, 128, 128, 59, 59, 59, 59, 59, 59, 59, 59, 59, 42, 42, 1, 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])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277526 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277526
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277526/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277526
Building REAL300025277527
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277527'
/scratch/stefan/7808390/working/building/REAL300025277527 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277527

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277527/0 /scratch/stefan/7808390/working/building/REAL300025277527 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/402
`/scratch/stefan/7808390/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)[C@H]2C[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277527 none CC1(CNC(=O)[C@H]2C[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
273  conformations in input
total number of sets (complete confs): 273
using faster count positions algorithm for large data
unique positions, atoms: [23, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 49, 65, 91, 91, 91, 91, 91, 23, 23, 23, 17, 17, 9, 1, 1, 3, 1, 1, 23, 23, 23, 23, 23, 23, 49, 49, 91] 273
rigid atoms, others: [33, 34, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277527 none CC1(CNC(=O)[C@H]2C[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
273  conformations in input
total number of sets (complete confs): 273
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 6, 6, 6, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 2, 2, 7, 13, 41, 41, 41, 41, 41, 2, 2, 2, 4, 4, 6, 23, 23, 69, 23, 23, 1, 1, 1, 1, 1, 1, 7, 7, 41] 273
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277527 none CC1(CNC(=O)[C@H]2C[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
273  conformations in input
total number of sets (complete confs): 273
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 58, 60, 60, 60, 91, 91, 91, 91, 91, 91, 41, 41, 41, 41, 31, 41, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 58, 58, 60, 91, 91, 273, 91, 91, 41, 41, 41, 41, 41, 41, 31, 31, 1] 273
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/7808390/working/building/REAL300025277527 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277527
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277527/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277527
Building REAL300025277528
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277528'
/scratch/stefan/7808390/working/building/REAL300025277528 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277528

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277528/0 /scratch/stefan/7808390/working/building/REAL300025277528 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/403
`/scratch/stefan/7808390/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277528 none CC1(C)CC1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 36, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 46, 46, 46, 46, 46, 64, 64, 64, 64, 64, 64, 64, 64, 64, 36, 36, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 46] 201
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
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: REAL300025277528 none CC1(C)CC1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 29, 29, 29, 47, 64, 64, 64, 64, 64, 64, 64, 64, 103, 145, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 29, 47, 47, 64, 64, 64, 64, 64, 64, 64, 64, 64, 103, 103, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 5] 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, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277528 none CC1(C)CC1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 111, 111, 111, 86, 46, 46, 46, 46, 46, 46, 46, 29, 46, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 111, 86, 86, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 1] 201
rigid atoms, others: [51, 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, 50])
total number of confs: 864
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277528 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277528
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277528/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277528
Building REAL300025277529
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277529'
/scratch/stefan/7808390/working/building/REAL300025277529 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277529

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277529/0 /scratch/stefan/7808390/working/building/REAL300025277529 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/404
`/scratch/stefan/7808390/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277529 none CCCCCCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 196, 191, 187, 166, 78, 78, 78, 53, 38, 38, 38, 38, 38, 38, 38, 25, 38, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 200, 197, 197, 191, 191, 188, 188, 166, 166, 78, 53, 53, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 1] 201
rigid atoms, others: [56, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
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: REAL300025277529 none CCCCCCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 59, 49, 52, 43, 32, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 60, 60, 60, 60, 60, 59, 58, 56, 56, 52, 52, 50, 50, 32, 32, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 38] 201
rigid atoms, others: [48, 17, 10, 11, 12, 13, 14, 15, 16, 49, 50, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56])
total number of confs: 457
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277529 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277529
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277529/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277529
Building REAL300025277530
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277530'
/scratch/stefan/7808390/working/building/REAL300025277530 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277530

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277530/0 /scratch/stefan/7808390/working/building/REAL300025277530 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/405
`/scratch/stefan/7808390/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(NC(N)=O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277530 none CC(NC(N)=O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 170, 201, 201, 201, 201, 170, 170, 145, 87, 87, 87, 87, 87, 87, 85, 35, 85, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 170, 145, 145, 87, 87, 87, 87, 87, 87, 87, 87, 87, 35, 35, 1] 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])
total number of confs: 835
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: REAL300025277530 none CC(NC(N)=O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 8, 26, 35, 35, 35, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 87, 87, 87, 87, 87, 26, 26, 26, 26, 35, 35, 35, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 87] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 270
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277530 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277530
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277530/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277530
Building REAL300025277531
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277531'
/scratch/stefan/7808390/working/building/REAL300025277531 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277531

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277531/0 /scratch/stefan/7808390/working/building/REAL300025277531 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/406
`/scratch/stefan/7808390/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(O)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277531 none CC1(CNC(=O)C2(O)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
453  conformations in input
total number of sets (complete confs): 453
using faster count positions algorithm for large data
unique positions, atoms: [32, 25, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 35, 35, 77, 101, 151, 151, 151, 151, 151, 32, 32, 32, 25, 25, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 77, 77, 151] 453
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 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])
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: REAL300025277531 none CC1(CNC(=O)C2(O)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
453  conformations in input
total number of sets (complete confs): 453
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 10, 10, 10, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 4, 4, 12, 20, 65, 65, 65, 65, 65, 2, 2, 2, 6, 6, 10, 96, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 12, 12, 65] 453
rigid atoms, others: [0, 1, 2, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 303
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: REAL300025277531 none CC1(CNC(=O)C2(O)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
453  conformations in input
total number of sets (complete confs): 453
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 100, 109, 109, 109, 151, 151, 151, 151, 151, 151, 65, 65, 65, 61, 37, 61, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 100, 100, 109, 453, 151, 151, 151, 151, 151, 151, 151, 151, 65, 65, 65, 65, 65, 65, 37, 37, 1] 453
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 1034
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277531 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277531
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277531/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277531
Building REAL300025277532
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277532'
/scratch/stefan/7808390/working/building/REAL300025277532 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277532

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277532/0 /scratch/stefan/7808390/working/building/REAL300025277532 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/407
`/scratch/stefan/7808390/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C#CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277532 none CN(C)C(=O)C#CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 61, 61, 61, 61, 61, 61, 59, 34, 59, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 73, 61, 61, 61, 61, 61, 61, 61, 61, 61, 34, 34, 1] 73
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277532 none CN(C)C(=O)C#CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 8, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 25, 61, 61, 61, 61, 61, 8, 8, 8, 8, 8, 8, 6, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 12, 61] 73
rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277532 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277532
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277532/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277532
Building REAL300025277533
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277533'
/scratch/stefan/7808390/working/building/REAL300025277533 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277533

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277533/0 /scratch/stefan/7808390/working/building/REAL300025277533 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/408
`/scratch/stefan/7808390/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277533 none C=C(C)CCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 156, 67, 67, 67, 51, 38, 38, 38, 38, 38, 38, 38, 27, 38, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 201, 188, 188, 156, 156, 67, 51, 51, 38, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 1] 201
rigid atoms, others: [51, 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, 50])
total number of confs: 957
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277533 none C=C(C)CCCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 73, 31, 24, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 73, 73, 73, 73, 73, 38, 39, 34, 34, 24, 24, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 38] 201
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277533 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277533
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277533/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277533
Building REAL300025277534
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277534'
/scratch/stefan/7808390/working/building/REAL300025277534 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277534

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277534/0 /scratch/stefan/7808390/working/building/REAL300025277534 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/409
`/scratch/stefan/7808390/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C)

`REAL300025277534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277534 none CC1=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 24, 79, 79, 79, 79, 79, 30, 30, 30, 30, 30, 30, 11, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 14, 14, 79, 30, 30, 30] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47])
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: REAL300025277534 none CC1=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 6, 6, 17, 30, 30, 30, 30, 30, 30, 38, 38, 90, 136, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 6, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 90, 90, 201, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 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: 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: REAL300025277534 none CC1=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 114, 79, 79, 79, 79, 79, 79, 64, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 138, 114, 114, 79, 79, 79, 79, 79, 79, 79, 79, 79, 31, 31, 1, 201, 201, 201] 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])
total number of confs: 626
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277534 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277534
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277534/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277534
Building REAL300025277535
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277535'
/scratch/stefan/7808390/working/building/REAL300025277535 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277535

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277535/0 /scratch/stefan/7808390/working/building/REAL300025277535 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/410
`/scratch/stefan/7808390/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC(F)C1)

`REAL300025277535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277535 none CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 46, 31, 31, 31, 31, 31] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277535 none CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 21, 31, 31, 31, 31, 31, 31, 34, 34, 77, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 77, 77, 201, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 22, 23, 24, 25] set([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, 42, 43])
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: REAL300025277535 none CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 84, 84, 84, 76, 46, 46, 46, 46, 46, 46, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 84, 76, 76, 46, 46, 46, 46, 46, 46, 46, 46, 46, 28, 28, 1, 201, 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])
total number of confs: 670
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277535 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277535
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277535/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277535
Building REAL300025277536
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277536'
/scratch/stefan/7808390/working/building/REAL300025277536 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277536

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277536/0 /scratch/stefan/7808390/working/building/REAL300025277536 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/411
`/scratch/stefan/7808390/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1)

`REAL300025277536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277536 none CCC1=CC=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens 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, 18, 18, 18, 18, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 75, 75, 75, 75, 75, 18, 40, 40, 40, 40, 40, 18, 18, 9, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 75, 18] 201
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49])
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: REAL300025277536 none CCC1=CC=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens 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, 5, 5, 5, 13, 18, 18, 18, 18, 18, 18, 19, 19, 47, 81, 193, 193, 193, 193, 193, 1, 6, 6, 6, 6, 6, 1, 1, 5, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 47, 47, 193, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 26] set([0, 7, 8, 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, 47, 48])
total number of confs: 428
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277536 none CCC1=CC=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 193, 193, 193, 193, 164, 164, 164, 135, 75, 75, 75, 75, 75, 75, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 193, 164, 135, 135, 75, 75, 75, 75, 75, 75, 75, 75, 75, 31, 31, 1, 193] 201
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])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277536 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277536
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277536/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277536
Building REAL300025277537
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277537'
/scratch/stefan/7808390/working/building/REAL300025277537 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277537

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277537/0 /scratch/stefan/7808390/working/building/REAL300025277537 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/412
`/scratch/stefan/7808390/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C#CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277537 none CC1(CNC(=O)C#CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [9, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 23, 32, 48, 48, 48, 48, 48, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 23, 23, 48] 48
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 36, 38, 39, 37] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277537 none CC1(CNC(=O)C#CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 9, 15, 33, 33, 33, 33, 33, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 33] 48
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
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: REAL300025277537 none CC1(CNC(=O)C#CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 33, 33, 33, 33, 25, 33, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 47, 47, 48, 48, 48, 48, 48, 48, 48, 48, 33, 33, 33, 33, 33, 33, 25, 25, 1] 48
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 189
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277537 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277537
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277537/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277537
Building REAL300025277538
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277538'
/scratch/stefan/7808390/working/building/REAL300025277538 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277538

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277538/0 /scratch/stefan/7808390/working/building/REAL300025277538 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/413
`/scratch/stefan/7808390/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277538 none C[C@@H]1C[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [51, 51, 51, 51, 8, 51, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 64, 64, 64, 64, 64, 51, 51, 51, 51, 51, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 64] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277538 none C[C@@H]1C[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 12, 12, 12, 35, 51, 51, 51, 51, 51, 51, 53, 53, 93, 128, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 35, 35, 51, 51, 51, 51, 51, 51, 51, 51, 51, 93, 93, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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, 44, 45])
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: REAL300025277538 none C[C@@H]1C[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 115, 201, 115, 115, 101, 64, 64, 64, 64, 64, 64, 59, 30, 59, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 115, 101, 101, 64, 64, 64, 64, 64, 64, 64, 64, 64, 30, 30, 1] 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])
total number of confs: 728
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277538 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277538
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277538/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277538
Building REAL300025277539
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277539'
/scratch/stefan/7808390/working/building/REAL300025277539 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277539

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277539/0 /scratch/stefan/7808390/working/building/REAL300025277539 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/414
`/scratch/stefan/7808390/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NC(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277539 none CNC(=O)NC(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 196, 141, 196, 141, 141, 115, 75, 75, 75, 75, 75, 75, 75, 33, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 196, 196, 141, 115, 115, 75, 75, 75, 75, 75, 75, 75, 75, 75, 33, 33, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 854
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: REAL300025277539 none CNC(=O)NC(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 28, 20, 8, 20, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 75, 75, 75, 75, 75, 32, 32, 32, 32, 28, 20, 20, 20, 20, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 75] 201
rigid atoms, others: [45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 236
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277539 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277539
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277539/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277539
Building REAL300025277540
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277540'
/scratch/stefan/7808390/working/building/REAL300025277540 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277540

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277540/0 /scratch/stefan/7808390/working/building/REAL300025277540 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/415
`/scratch/stefan/7808390/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277540 none CCN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [41, 24, 24, 24, 24, 24, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 45, 45, 45, 45, 45, 41, 41, 41, 41, 41, 24, 17, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 45] 201
rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277540 none CCN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 4, 4, 4, 11, 24, 24, 24, 24, 24, 24, 24, 24, 45, 71, 165, 165, 165, 165, 165, 3, 3, 3, 3, 3, 1, 4, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 45, 45, 165] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 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, 46, 47])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277540 none CCN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 165, 165, 165, 165, 165, 165, 165, 165, 103, 45, 45, 45, 45, 45, 45, 45, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 165, 165, 103, 103, 45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 30, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/7808390/working/building/REAL300025277540 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277540
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277540/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277540
Building REAL300025277541
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277541'
/scratch/stefan/7808390/working/building/REAL300025277541 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277541

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277541/0 /scratch/stefan/7808390/working/building/REAL300025277541 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/416
`/scratch/stefan/7808390/working/3D/416' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(C3CCC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277541 none CC1(CNC(=O)C2(C3CCC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 3, 3, 1, 3, 1, 1, 9, 9, 9, 1, 1, 17, 17, 17, 17, 17, 17, 17, 43, 58, 104, 104, 104, 104, 104, 17, 17, 17, 11, 11, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 43, 43, 104] 115
rigid atoms, others: [43, 4, 6, 7, 40, 41, 42, 11, 12] set([0, 1, 2, 3, 5, 8, 9, 10, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 301
number of broken/clashed sets: 1
./output.2.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: REAL300025277541 none CC1(CNC(=O)C2(C3CCC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 66, 79, 79, 79, 104, 115, 115, 115, 104, 104, 44, 44, 44, 44, 31, 44, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 66, 66, 79, 115, 115, 115, 115, 115, 115, 115, 104, 104, 104, 104, 44, 44, 44, 44, 44, 44, 31, 31, 1] 115
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 455
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277541 none CC1(CNC(=O)C2(C3CCC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 17, 39, 39, 39, 17, 17, 1, 1, 1, 1, 1, 2, 2, 7, 13, 44, 44, 44, 44, 44, 2, 2, 2, 5, 5, 9, 39, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 44] 115
rigid atoms, others: [0, 1, 2, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 50, 51, 52])
total number of confs: 207
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: REAL300025277541 none CC1(CNC(=O)C2(C3CCC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [39, 31, 15, 15, 9, 15, 1, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 39, 39, 72, 80, 115, 115, 115, 115, 115, 39, 39, 39, 31, 31, 15, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 72, 72, 115] 115
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 39, 38] set([0, 1, 2, 3, 4, 5, 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, 51, 52])
total number of confs: 384
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277541 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277541
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277541/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277541
Building REAL300025277542
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277542'
/scratch/stefan/7808390/working/building/REAL300025277542 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277542

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277542/0 /scratch/stefan/7808390/working/building/REAL300025277542 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/417
`/scratch/stefan/7808390/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)[C@@H]2CC[C@@H]3C[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277542 none CC1(CNC(=O)[C@@H]2CC[C@@H]3C[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [12, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 32, 44, 63, 63, 63, 63, 63, 12, 12, 12, 8, 8, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 32, 32, 63] 63
rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 187
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277542 none CC1(CNC(=O)[C@@H]2CC[C@@H]3C[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 2, 2, 8, 14, 41, 41, 41, 41, 41, 2, 2, 2, 5, 5, 9, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 8, 8, 41] 63
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 121
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277542 none CC1(CNC(=O)[C@@H]2CC[C@@H]3C[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 61, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 41, 41, 41, 41, 31, 41, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 61, 61, 63, 63, 63, 63, 63, 63, 63, 41, 41, 41, 41, 41, 41, 31, 31, 1] 63
rigid atoms, others: [49, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 252
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277542 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277542
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277542/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277542
Building REAL300025277543
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277543'
/scratch/stefan/7808390/working/building/REAL300025277543 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277543

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277543/0 /scratch/stefan/7808390/working/building/REAL300025277543 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/418
`/scratch/stefan/7808390/working/3D/418' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)COC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277543 none CC1(CNC(=O)COC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [133, 103, 73, 73, 22, 73, 6, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 178, 182, 201, 201, 201, 201, 201, 133, 133, 133, 103, 103, 73, 22, 22, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 178, 178, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 774
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277543 none CC1(CNC(=O)COC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 6, 6, 6, 37, 95, 133, 133, 133, 1, 1, 1, 1, 1, 2, 2, 5, 7, 24, 24, 24, 24, 24, 2, 2, 2, 3, 3, 6, 37, 37, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 5, 5, 24] 201
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 407
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: REAL300025277543 none CC1(CNC(=O)COC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 28, 49, 49, 49, 128, 178, 201, 201, 201, 24, 24, 24, 24, 18, 24, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 28, 28, 49, 128, 128, 201, 201, 201, 201, 201, 24, 24, 24, 24, 24, 24, 18, 18, 1] 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])
total number of confs: 685
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277543 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277543
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277543/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277543
Building REAL300025277544
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277544'
/scratch/stefan/7808390/working/building/REAL300025277544 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277544

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277544/0 /scratch/stefan/7808390/working/building/REAL300025277544 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/419
`/scratch/stefan/7808390/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@]2(C(=O)NCC3(C)CCCN3C(=O)CSC3=NNC(=O)[N-]3)C[C@H]12)

`REAL300025277544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277544 none C[C@@H]1C[C@]2(C(=O)NCC3(C)CCCN3C(=O)CSC3=NNC(=O)[N-]3)C[C@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 56, 56, 56, 56, 56, 33, 33, 33, 33, 33, 33, 33, 33, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 56, 33, 33] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277544 none C[C@@H]1C[C@]2(C(=O)NCC3(C)CCCN3C(=O)CSC3=NNC(=O)[N-]3)C[C@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 23, 33, 33, 33, 33, 33, 33, 36, 36, 78, 119, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 23, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 78, 78, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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: REAL300025277544 none C[C@@H]1C[C@]2(C(=O)NCC3(C)CCCN3C(=O)CSC3=NNC(=O)[N-]3)C[C@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 127, 127, 127, 107, 56, 56, 56, 56, 56, 56, 52, 31, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 127, 107, 107, 56, 56, 56, 56, 56, 56, 56, 56, 56, 31, 31, 1, 201, 201] 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])
total number of confs: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277544 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277544
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277544/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277544
Building REAL300025277545
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277545'
/scratch/stefan/7808390/working/building/REAL300025277545 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277545

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277545/0 /scratch/stefan/7808390/working/building/REAL300025277545 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/420
`/scratch/stefan/7808390/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277545 none CNC(=O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 192, 201, 137, 137, 137, 98, 56, 56, 56, 56, 56, 56, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 192, 192, 137, 98, 98, 56, 56, 56, 56, 56, 56, 56, 56, 56, 31, 31, 1] 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])
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: REAL300025277545 none CNC(=O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [60, 60, 25, 60, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 56, 56, 56, 56, 56, 60, 60, 60, 60, 25, 25, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 56] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277545 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277545
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277545/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277545
Building REAL300025277546
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277546'
/scratch/stefan/7808390/working/building/REAL300025277546 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277546

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277546/0 /scratch/stefan/7808390/working/building/REAL300025277546 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/421
`/scratch/stefan/7808390/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1COC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277546 none CC(OC1COC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 36, 64, 64, 64, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 53, 53, 53, 53, 53, 16, 16, 16, 16, 64, 64, 64, 64, 64, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 53] 201
rigid atoms, others: [45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
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: REAL300025277546 none CC(OC1COC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 15, 28, 28, 28, 46, 64, 64, 64, 64, 64, 64, 64, 64, 106, 146, 201, 201, 201, 201, 201, 15, 15, 15, 15, 1, 1, 1, 1, 1, 28, 46, 46, 64, 64, 64, 64, 64, 64, 64, 64, 64, 106, 106, 201] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 35, 31] set([0, 1, 7, 8, 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, 47, 48, 49, 50])
total number of confs: 669
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277546 none CC(OC1COC1)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [168, 127, 168, 186, 201, 201, 201, 127, 127, 85, 53, 53, 53, 53, 53, 53, 53, 31, 53, 13, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 201, 201, 201, 127, 85, 85, 53, 53, 53, 53, 53, 53, 53, 53, 53, 31, 31, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 842
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277546 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277546
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277546/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277546
Building REAL300025277547
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277547'
/scratch/stefan/7808390/working/building/REAL300025277547 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277547

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277547/0 /scratch/stefan/7808390/working/building/REAL300025277547 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/422
`/scratch/stefan/7808390/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277547 none CN1C(=O)CCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 20, 84, 84, 84, 84, 84, 28, 28, 28, 28, 28, 28, 28, 28, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 84] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277547 none CN1C(=O)CCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 28, 28, 28, 28, 28, 28, 37, 37, 72, 117, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 72, 72, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277547 none CN1C(=O)CCC1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 176, 176, 128, 84, 84, 84, 84, 84, 84, 72, 33, 72, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 176, 128, 128, 84, 84, 84, 84, 84, 84, 84, 84, 84, 33, 33, 1] 201
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277547 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277547
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277547/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277547
Building REAL300025277548
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277548'
/scratch/stefan/7808390/working/building/REAL300025277548 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277548

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277548/0 /scratch/stefan/7808390/working/building/REAL300025277548 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/423
`/scratch/stefan/7808390/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CN(CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277548 none CCC1CN(CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 25, 25, 24, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 55, 55, 55, 55, 55, 25, 36, 36, 36, 36, 36, 25, 25, 25, 24, 24, 8, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 55, 25, 25] 201
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51, 52, 53])
total number of confs: 242
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277548 none CCC1CN(CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 8, 8, 8, 17, 25, 25, 25, 25, 25, 25, 25, 25, 57, 92, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 1, 1, 1, 5, 5, 8, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 57, 57, 201, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 52, 53, 26] set([0, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 487
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277548 none CCC1CN(CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 127, 127, 127, 80, 55, 55, 55, 55, 55, 55, 55, 40, 55, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 80, 80, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 40, 1, 201, 201] 201
rigid atoms, others: [51, 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, 50, 52, 53])
total number of confs: 890
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277548 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277548/1 /scratch/stefan/7808390/working/building/REAL300025277548 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/424
`/scratch/stefan/7808390/working/3D/424' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1C[NH+](CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277548.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277548/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277548 none CCC1C[NH+](CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [21, 18, 18, 18, 11, 18, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 16, 16, 16, 16, 16, 18, 21, 21, 21, 21, 21, 18, 18, 18, 11, 11, 6, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 16, 18, 18] 37
rigid atoms, others: [48, 17, 47, 44, 10, 11, 12, 13, 14, 45, 16, 49, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52, 53, 54])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277548 none CCC1C[NH+](CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 17, 18, 18, 18, 18, 18, 18, 23, 23, 33, 33, 37, 37, 37, 37, 37, 1, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 8, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 33, 33, 37, 1, 1] 37
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 35, 53, 54, 27] set([0, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277548 none CCC1C[NH+](CC(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 27, 37, 22, 22, 22, 18, 16, 16, 16, 16, 16, 16, 16, 13, 16, 10, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 27, 22, 18, 18, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 1, 37, 37] 37
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54])
total number of confs: 129
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277548 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277548
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277548/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277548/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277548
Building REAL300025277549
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277549'
/scratch/stefan/7808390/working/building/REAL300025277549 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277549

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277549/0 /scratch/stefan/7808390/working/building/REAL300025277549 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/425
`/scratch/stefan/7808390/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(C)C=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277549 none CC1=CN(C)C=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 24, 89, 89, 89, 89, 89, 33, 33, 33, 33, 33, 33, 33, 33, 11, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 14, 14, 89] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277549 none CC1=CN(C)C=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 33, 33, 33, 33, 33, 33, 39, 39, 84, 132, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 10, 22, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 84, 84, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 555
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277549 none CC1=CN(C)C=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 169, 169, 139, 89, 89, 89, 89, 89, 89, 75, 32, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 169, 139, 139, 89, 89, 89, 89, 89, 89, 89, 89, 89, 32, 32, 1] 201
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277549 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277549
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277549/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277549
Building REAL300025277550
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277550'
/scratch/stefan/7808390/working/building/REAL300025277550 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277550

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277550/0 /scratch/stefan/7808390/working/building/REAL300025277550 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/426
`/scratch/stefan/7808390/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC=CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277550 none C=CC=CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 186, 96, 96, 96, 71, 45, 45, 45, 45, 45, 45, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 96, 71, 71, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 29, 1] 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])
total number of confs: 866
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277550 none C=CC=CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [62, 62, 62, 33, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 45, 45, 45, 45, 45, 62, 62, 62, 62, 62, 33, 33, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 45] 201
rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277550 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277550
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277550/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277550
Building REAL300025277551
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277551'
/scratch/stefan/7808390/working/building/REAL300025277551 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277551

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277551/0 /scratch/stefan/7808390/working/building/REAL300025277551 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/427
`/scratch/stefan/7808390/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1)

`REAL300025277551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277551 none C#CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 19, 68, 68, 68, 68, 68, 30, 30, 30, 30, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 68, 30, 30, 30, 30, 30, 30] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277551 none C#CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 20, 30, 30, 30, 30, 30, 30, 36, 36, 81, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 81, 81, 201, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 45, 46, 47, 23, 24, 25, 26] set([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: 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: REAL300025277551 none C#CC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CCC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 110, 110, 110, 98, 68, 68, 68, 68, 68, 68, 57, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 110, 98, 98, 68, 68, 68, 68, 68, 68, 68, 68, 68, 28, 28, 1, 201, 201, 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])
total number of confs: 689
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277551 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277551
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277551/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277551
Building REAL300025277552
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277552'
/scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277552

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277552/0 /scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/428
`/scratch/stefan/7808390/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277552 none C[N@@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 10, 17, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 40, 40, 40, 40, 40, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 12, 40] 48
rigid atoms, others: [48, 45, 43, 44, 11, 12, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 144
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: REAL300025277552 none C[N@@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 17, 17, 17, 17, 17, 17, 17, 17, 27, 35, 48, 48, 48, 48, 48, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 27, 27, 48] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 146
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: REAL300025277552 none C[N@@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 44, 40, 40, 40, 40, 40, 40, 35, 18, 35, 11, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 44, 44, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 1] 48
rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 145
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277552/1 /scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/429
`/scratch/stefan/7808390/working/3D/429' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277552.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277552/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277552 none C[N@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 16] 19
rigid atoms, others: [48, 45, 43, 44, 11, 12, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277552 none C[N@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 13, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277552 none C[N@H+]1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 16, 14, 16, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 1] 19
rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 55
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277552/2 /scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/430
`/scratch/stefan/7808390/working/3D/430' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277552.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277552/2/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: REAL300025277552 none CN1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 28, 14, 28, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 26, 105, 105, 105, 105, 105, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 105] 201
rigid atoms, others: [45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
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: REAL300025277552 none CN1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 28, 28, 28, 28, 28, 28, 40, 40, 87, 133, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 87, 87, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277552 none CN1CCC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 169, 105, 105, 105, 105, 105, 105, 79, 32, 79, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 169, 169, 105, 105, 105, 105, 105, 105, 105, 105, 105, 32, 32, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 710
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277552 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277552
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277552/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277552/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277552/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277552
Building REAL300025277553
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277553'
/scratch/stefan/7808390/working/building/REAL300025277553 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277553

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277553/0 /scratch/stefan/7808390/working/building/REAL300025277553 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/431
`/scratch/stefan/7808390/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC=CC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277553 none CCCC=CC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 163, 163, 123, 100, 123, 100, 100, 69, 52, 52, 52, 52, 52, 52, 52, 38, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 163, 163, 123, 369, 100, 69, 69, 52, 52, 52, 52, 52, 52, 52, 52, 52, 38, 38, 1] 603
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 1280
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277553 none CCCC=CC(O)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [39, 35, 21, 21, 7, 5, 7, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 52, 52, 52, 52, 52, 39, 39, 39, 39, 39, 35, 35, 21, 21, 7, 21, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 52] 603
rigid atoms, others: [48, 17, 47, 44, 10, 11, 12, 13, 14, 45, 16, 49, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277553 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277553
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277553/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277553
Building REAL300025277554
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277554'
/scratch/stefan/7808390/working/building/REAL300025277554 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277554

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277554/0 /scratch/stefan/7808390/working/building/REAL300025277554 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/432
`/scratch/stefan/7808390/working/3D/432' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CC=CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277554 none CC1(CNC(=O)C2CC=CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [42, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 46, 46, 100, 126, 173, 173, 173, 173, 173, 42, 42, 42, 27, 27, 10, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 100, 100, 173] 173
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 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])
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: REAL300025277554 none CC1(CNC(=O)C2CC=CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 12, 12, 12, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 4, 4, 11, 24, 82, 82, 82, 82, 82, 2, 2, 2, 6, 6, 12, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 11, 11, 82] 173
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277554 none CC1(CNC(=O)C2CC=CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 125, 140, 140, 140, 173, 173, 173, 173, 173, 82, 82, 82, 79, 40, 79, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 125, 125, 140, 173, 173, 173, 173, 173, 173, 173, 82, 82, 82, 82, 82, 82, 40, 40, 1] 173
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])
total number of confs: 669
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277554 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277554
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277554/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277554
Building REAL300025277555
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277555'
/scratch/stefan/7808390/working/building/REAL300025277555 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277555

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277555/0 /scratch/stefan/7808390/working/building/REAL300025277555 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/433
`/scratch/stefan/7808390/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CCCO)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277555 none CC(C)(CCCO)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [185, 142, 185, 185, 201, 201, 201, 142, 142, 86, 53, 53, 53, 53, 53, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 185, 201, 201, 201, 201, 201, 201, 603, 142, 86, 86, 53, 53, 53, 53, 53, 53, 53, 53, 53, 28, 28, 1] 603
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 1494
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: REAL300025277555 none CC(C)(CCCO)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [17, 10, 17, 17, 25, 25, 43, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 53, 53, 53, 53, 53, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 43, 43, 129, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 53] 603
rigid atoms, others: [48, 17, 10, 11, 12, 13, 14, 47, 16, 49, 50, 51, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54])
total number of confs: 416
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277555 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277555
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277555/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277555
Building REAL300025277556
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277556'
/scratch/stefan/7808390/working/building/REAL300025277556 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277556

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277556/0 /scratch/stefan/7808390/working/building/REAL300025277556 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/434
`/scratch/stefan/7808390/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCOC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277556 none CC1(CNC(=O)CCOC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [119, 102, 77, 77, 20, 77, 20, 5, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 140, 154, 201, 201, 201, 201, 201, 119, 119, 119, 102, 102, 77, 20, 20, 20, 20, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 140, 140, 201] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 651
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277556 none CC1(CNC(=O)CCOC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 6, 6, 6, 36, 36, 93, 119, 119, 1, 1, 1, 1, 1, 2, 2, 5, 10, 37, 37, 37, 37, 37, 2, 2, 2, 3, 3, 6, 36, 36, 36, 36, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 5, 5, 37] 201
rigid atoms, others: [0, 1, 2, 41, 42, 43, 12, 13, 14, 15, 16, 46, 45, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277556 none CC1(CNC(=O)CCOC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 69, 69, 69, 160, 160, 195, 201, 201, 37, 37, 37, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 69, 160, 160, 160, 160, 201, 201, 201, 201, 201, 37, 37, 37, 37, 37, 37, 29, 29, 1] 201
rigid atoms, others: [49, 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])
total number of confs: 744
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277556 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277556
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277556/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277556
Building REAL300025277557
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277557'
/scratch/stefan/7808390/working/building/REAL300025277557 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277557

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277557/0 /scratch/stefan/7808390/working/building/REAL300025277557 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/435
`/scratch/stefan/7808390/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCCCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277557 none CC1(CNC(=O)CCCCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [36, 36, 36, 44, 58, 58, 58, 151, 178, 182, 199, 201, 36, 36, 36, 36, 30, 36, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 44, 44, 58, 151, 151, 180, 180, 182, 182, 201, 201, 201, 201, 603, 36, 36, 36, 36, 36, 36, 30, 30, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1513
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277557 none CC1(CNC(=O)CCCCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 3, 7, 7, 7, 37, 49, 60, 71, 102, 1, 1, 1, 1, 1, 2, 2, 5, 10, 36, 36, 36, 36, 36, 2, 2, 2, 3, 3, 7, 37, 37, 57, 57, 60, 60, 79, 79, 101, 98, 306, 1, 1, 1, 1, 1, 1, 5, 5, 36] 603
rigid atoms, others: [0, 1, 2, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 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, 49, 50, 51])
total number of confs: 958
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277557 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277557
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277557/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277557
Building REAL300025277558
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277558'
/scratch/stefan/7808390/working/building/REAL300025277558 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277558

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277558/0 /scratch/stefan/7808390/working/building/REAL300025277558 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/436
`/scratch/stefan/7808390/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277558 none CC1(CNC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 28, 28, 69, 90, 132, 132, 132, 132, 132, 24, 24, 24, 13, 13, 5, 1, 1, 24, 24, 24, 24, 24, 24, 69, 69, 132] 132
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 387
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277558 none CC1(CNC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 16, 16, 16, 24, 24, 24, 24, 1, 1, 1, 1, 1, 4, 4, 14, 28, 90, 90, 90, 90, 90, 2, 2, 2, 7, 7, 16, 24, 24, 1, 1, 1, 1, 1, 1, 14, 14, 90] 132
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 11, 12, 34, 14, 13, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 222
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277558 none CC1(CNC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 120, 132, 132, 132, 132, 132, 132, 132, 90, 90, 90, 84, 41, 84, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 120, 120, 132, 132, 132, 90, 90, 90, 90, 90, 90, 41, 41, 1] 132
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])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277558 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277558
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277558/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277558
Building REAL300025277559
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277559'
/scratch/stefan/7808390/working/building/REAL300025277559 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277559

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277559/0 /scratch/stefan/7808390/working/building/REAL300025277559 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/437
`/scratch/stefan/7808390/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C[NH+]2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277559 none CC1(CNC(=O)C[NH+]2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 25, 14, 14, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 30, 30, 37, 38, 42, 42, 42, 42, 42, 27, 27, 27, 25, 25, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 37, 37, 42] 42
rigid atoms, others: [45, 43, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 44, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 164
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277559 none CC1(CNC(=O)C[NH+]2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 10, 10, 10, 24, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 10, 16, 34, 34, 34, 34, 34, 2, 2, 2, 4, 4, 10, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 10, 10, 34] 42
rigid atoms, others: [0, 1, 2, 49, 48, 18, 14, 15, 16, 17, 50, 51, 46, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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, 52, 53, 54])
total number of confs: 179
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277559 none CC1(CNC(=O)C[NH+]2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 35, 37, 37, 37, 42, 42, 42, 42, 42, 42, 42, 34, 34, 34, 32, 25, 32, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 35, 35, 37, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 34, 25, 25, 1] 42
rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 151
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277559 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277559/1 /scratch/stefan/7808390/working/building/REAL300025277559 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/438
`/scratch/stefan/7808390/working/3D/438' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CN2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277559.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277559/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277559 none CC1(CNC(=O)CN2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 58, 31, 31, 8, 31, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 104, 107, 126, 126, 126, 126, 126, 74, 74, 74, 58, 58, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 104, 104, 126] 126
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 43, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53])
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: REAL300025277559 none CC1(CNC(=O)CN2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 6, 6, 6, 33, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 2, 2, 5, 7, 24, 24, 24, 24, 24, 2, 2, 2, 3, 3, 6, 33, 33, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 5, 5, 24] 126
rigid atoms, others: [0, 1, 2, 17, 48, 47, 13, 14, 45, 16, 49, 50, 46, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 51, 52, 53])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277559 none CC1(CNC(=O)CN2CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 28, 47, 47, 47, 101, 126, 126, 126, 126, 126, 24, 24, 24, 24, 18, 24, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 28, 28, 47, 101, 101, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 24, 24, 24, 24, 24, 24, 18, 18, 1] 126
rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 451
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277559 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277559
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277559/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277559/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277559
Building REAL300025277560
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277560'
/scratch/stefan/7808390/working/building/REAL300025277560 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277560

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277560/0 /scratch/stefan/7808390/working/building/REAL300025277560 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/439
`/scratch/stefan/7808390/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277560 none CC1(CNC(=O)C2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [28, 17, 6, 5, 1, 5, 1, 1, 8, 1, 1, 1, 28, 28, 28, 28, 28, 31, 31, 86, 122, 201, 201, 201, 201, 201, 28, 28, 28, 17, 17, 6, 8, 8, 24, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 86, 86, 201] 603
rigid atoms, others: [35, 4, 37, 6, 7, 40, 9, 10, 11, 36, 38, 39] set([0, 1, 2, 3, 5, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 591
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: REAL300025277560 none CC1(CNC(=O)C2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 5, 10, 10, 10, 28, 49, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 11, 23, 86, 86, 86, 86, 86, 2, 2, 2, 5, 5, 10, 49, 49, 147, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 11, 11, 86] 603
rigid atoms, others: [0, 1, 2, 41, 42, 43, 12, 13, 14, 15, 16, 46, 45, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 476
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277560 none CC1(CNC(=O)C2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [86, 86, 86, 119, 138, 138, 138, 201, 201, 201, 201, 201, 86, 86, 86, 84, 38, 84, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 119, 119, 138, 201, 201, 603, 201, 201, 201, 201, 201, 201, 86, 86, 86, 86, 86, 86, 38, 38, 1] 603
rigid atoms, others: [49, 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])
total number of confs: 1366
number of broken/clashed sets: 105
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277560 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277560
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277560/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277560
Building REAL300025277561
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277561'
/scratch/stefan/7808390/working/building/REAL300025277561 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277561

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277561/0 /scratch/stefan/7808390/working/building/REAL300025277561 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/440
`/scratch/stefan/7808390/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CCCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277561 none CC1(CNC(=O)C2CCCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
213  conformations in input
total number of sets (complete confs): 213
using faster count positions algorithm for large data
unique positions, atoms: [24, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 45, 53, 71, 71, 71, 71, 71, 24, 24, 24, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 24, 24, 24, 24, 24, 24, 45, 45, 71] 213
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 230
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277561 none CC1(CNC(=O)C2CCCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
213  conformations in input
total number of sets (complete confs): 213
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 8, 8, 8, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 2, 2, 8, 14, 36, 36, 36, 36, 36, 2, 2, 2, 4, 4, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 72, 1, 1, 1, 1, 1, 1, 8, 8, 36] 213
rigid atoms, others: [0, 1, 2, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 50, 51, 52])
total number of confs: 215
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: REAL300025277561 none CC1(CNC(=O)C2CCCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
213  conformations in input
total number of sets (complete confs): 213
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 53, 56, 56, 56, 71, 71, 71, 71, 71, 71, 36, 36, 36, 36, 28, 36, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 53, 53, 56, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 213, 36, 36, 36, 36, 36, 36, 28, 28, 1] 213
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 487
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277561 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277561
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277561/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277561
Building REAL300025277562
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277562'
/scratch/stefan/7808390/working/building/REAL300025277562 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277562

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277562/0 /scratch/stefan/7808390/working/building/REAL300025277562 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/441
`/scratch/stefan/7808390/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CN=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277562 none CN1C=CN=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 43, 43, 39, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 16, 61, 61, 61, 61, 61, 43, 43, 43, 43, 43, 39, 39, 12, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 61] 201
rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
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: REAL300025277562 none CN1C=CN=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 13, 13, 13, 27, 43, 43, 43, 43, 43, 43, 43, 43, 71, 115, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 13, 27, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 71, 71, 201] 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, 47, 48])
total number of confs: 542
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277562 none CN1C=CN=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 149, 149, 149, 92, 61, 61, 61, 61, 61, 61, 61, 32, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 149, 92, 92, 61, 61, 61, 61, 61, 61, 61, 61, 61, 32, 32, 1] 201
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/7808390/working/building/REAL300025277562 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277562
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277562/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277562
Building REAL300025277563
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277563'
/scratch/stefan/7808390/working/building/REAL300025277563 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277563

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277563/0 /scratch/stefan/7808390/working/building/REAL300025277563 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/442
`/scratch/stefan/7808390/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@@H+]1C)

`REAL300025277563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277563 none CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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]
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: [14, 14, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 14, 14, 14, 14, 14, 14, 14] 35
rigid atoms, others: [11, 6, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 120
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277563 none CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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]
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, 6, 6, 6, 12, 14, 14, 14, 14, 14, 14, 15, 15, 21, 24, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 21, 35, 1, 1, 1, 1, 2, 2, 2] 35
rigid atoms, others: [0, 1, 2, 3, 32, 48, 49, 50, 51, 23, 24, 25, 26, 27, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54])
total number of confs: 121
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: REAL300025277563 none CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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]
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, 34, 34, 34, 34, 34, 34, 30, 18, 30, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 18, 1, 35, 35, 35, 35, 35, 35, 35] 35
rigid atoms, others: [47, 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, 46, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 107
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277563 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277563/1 /scratch/stefan/7808390/working/building/REAL300025277563 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/443
`/scratch/stefan/7808390/working/3D/443' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC[N@H+]1C)

`REAL300025277563.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277563/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277563 none CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 29, 73, 73, 73, 73, 73, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 73, 25, 25, 25, 25, 25, 25, 25] 94
rigid atoms, others: [11, 6, 7, 8, 9, 10, 39, 12, 13, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 211
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277563 none CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 19, 25, 25, 25, 25, 25, 25, 26, 26, 42, 60, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8, 19, 19, 25, 25, 25, 25, 25, 25, 25, 25, 25, 42, 42, 94, 1, 1, 1, 1, 2, 2, 2] 94
rigid atoms, others: [0, 1, 2, 3, 32, 48, 49, 50, 51, 23, 24, 25, 26, 27, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54])
total number of confs: 269
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: REAL300025277563 none CC1C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 92, 92, 92, 80, 73, 73, 73, 73, 73, 73, 62, 27, 62, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 92, 80, 80, 73, 73, 73, 73, 73, 73, 73, 73, 73, 27, 27, 1, 94, 94, 94, 94, 94, 94, 94] 94
rigid atoms, others: [47, 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, 46, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 309
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277563 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277563
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277563/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277563/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277563
Building REAL300025277564
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277564'
/scratch/stefan/7808390/working/building/REAL300025277564 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277564

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277564/0 /scratch/stefan/7808390/working/building/REAL300025277564 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/444
`/scratch/stefan/7808390/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CN=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277564 none CC1(CNC(=O)C2=CN=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [37, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 43, 43, 81, 102, 145, 145, 145, 145, 145, 37, 37, 37, 27, 27, 10, 1, 1, 1, 37, 37, 37, 37, 37, 37, 81, 81, 145] 145
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 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: REAL300025277564 none CC1(CNC(=O)C2=CN=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 4, 4, 13, 20, 66, 66, 66, 66, 66, 2, 2, 2, 5, 5, 9, 37, 37, 37, 1, 1, 1, 1, 1, 1, 13, 13, 66] 145
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 189
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: REAL300025277564 none CC1(CNC(=O)C2=CN=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 87, 98, 98, 98, 145, 145, 145, 145, 145, 145, 66, 66, 66, 62, 40, 62, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 87, 87, 98, 145, 145, 145, 66, 66, 66, 66, 66, 66, 40, 40, 1] 145
rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 460
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277564 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277564
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277564/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277564
Building REAL300025277565
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277565'
/scratch/stefan/7808390/working/building/REAL300025277565 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277565

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277565/0 /scratch/stefan/7808390/working/building/REAL300025277565 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/445
`/scratch/stefan/7808390/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CNC(=O)S2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277565 none CC1(CNC(=O)C2=CNC(=O)S2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [34, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 39, 39, 82, 112, 165, 165, 165, 165, 165, 34, 34, 34, 23, 23, 10, 1, 1, 34, 34, 34, 34, 34, 34, 82, 82, 165] 165
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 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: REAL300025277565 none CC1(CNC(=O)C2=CNC(=O)S2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 13, 13, 13, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 4, 4, 13, 29, 93, 93, 93, 93, 93, 2, 2, 2, 6, 6, 13, 34, 34, 1, 1, 1, 1, 1, 1, 13, 13, 93] 165
rigid atoms, others: [0, 1, 2, 34, 36, 37, 38, 39, 12, 13, 14, 15, 16, 35] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277565 none CC1(CNC(=O)C2=CNC(=O)S2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 142, 149, 149, 149, 165, 165, 165, 165, 165, 93, 93, 93, 88, 38, 88, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 142, 142, 149, 165, 165, 93, 93, 93, 93, 93, 93, 38, 38, 1] 165
rigid atoms, others: [42, 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])
total number of confs: 602
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277565 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277565
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277565/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277565
Building REAL300025277566
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277566'
/scratch/stefan/7808390/working/building/REAL300025277566 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277566

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277566/0 /scratch/stefan/7808390/working/building/REAL300025277566 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/446
`/scratch/stefan/7808390/working/3D/446' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277566 none CC1(CNC(=O)CCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 43, 66, 66, 66, 129, 152, 156, 156, 34, 34, 34, 34, 26, 34, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 43, 43, 66, 129, 129, 152, 152, 156, 156, 34, 34, 34, 34, 34, 34, 26, 26, 1] 156
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])
total number of confs: 673
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277566 none CC1(CNC(=O)CCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 39, 60, 87, 88, 1, 1, 1, 1, 1, 2, 2, 5, 10, 34, 34, 34, 34, 34, 2, 2, 2, 3, 3, 7, 39, 39, 60, 60, 88, 87, 1, 1, 1, 1, 1, 1, 5, 5, 34] 156
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 415
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277566 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277566
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277566/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277566
Building REAL300025277567
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277567'
/scratch/stefan/7808390/working/building/REAL300025277567 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277567

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277567/0 /scratch/stefan/7808390/working/building/REAL300025277567 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/447
`/scratch/stefan/7808390/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025277567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277567 none C=CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 20, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 20, 20, 50, 50, 50, 33, 33, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 44, 20, 20, 20, 20] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277567 none C=CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 6, 6, 6, 12, 20, 20, 20, 20, 20, 20, 20, 20, 52, 85, 182, 182, 182, 182, 182, 1, 1, 11, 11, 11, 4, 4, 6, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 52, 52, 182, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 46, 47, 48, 49, 24, 25] set([0, 1, 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, 43, 44, 45])
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: REAL300025277567 none C=CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 92, 92, 92, 70, 44, 44, 44, 44, 44, 44, 44, 28, 44, 12, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 92, 70, 70, 44, 44, 44, 44, 44, 44, 44, 44, 44, 28, 28, 1, 182, 182, 182, 182] 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: 769
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277567 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277567
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277567/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277567
Building REAL300025277568
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277568'
/scratch/stefan/7808390/working/building/REAL300025277568 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277568

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277568/0 /scratch/stefan/7808390/working/building/REAL300025277568 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/448
`/scratch/stefan/7808390/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)COC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277568 none CC1(CNC(=O)COC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 12, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 33, 60, 60, 60, 151, 179, 179, 179, 30, 30, 30, 29, 21, 29, 12, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 33, 33, 60, 151, 151, 179, 30, 30, 30, 30, 30, 30, 21, 21, 1] 179
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])
total number of confs: 651
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: REAL300025277568 none CC1(CNC(=O)COC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 12, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 41, 99, 128, 128, 1, 1, 1, 1, 1, 3, 3, 6, 8, 30, 30, 30, 30, 30, 2, 2, 2, 3, 3, 7, 41, 41, 128, 1, 1, 1, 1, 1, 1, 6, 6, 30] 179
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 11, 12, 34, 14, 13, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 447
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277568 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277568
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277568/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277568
Building REAL300025277569
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277569'
/scratch/stefan/7808390/working/building/REAL300025277569 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277569

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277569/0 /scratch/stefan/7808390/working/building/REAL300025277569 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/449
`/scratch/stefan/7808390/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277569 none CC1(CNC(=O)C2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [34, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 36, 36, 69, 94, 129, 129, 129, 129, 129, 34, 34, 34, 25, 25, 9, 2, 2, 2, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 69, 69, 129] 129
rigid atoms, others: [11, 4, 37, 6, 7, 8, 9, 10, 39, 12, 40, 36, 38] set([0, 1, 2, 3, 5, 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])
total number of confs: 392
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277569 none CC1(CNC(=O)C2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 12, 12, 12, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 4, 4, 11, 18, 67, 67, 67, 67, 67, 2, 2, 2, 6, 6, 12, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 11, 11, 67] 129
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 212
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: REAL300025277569 none CC1(CNC(=O)C2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [67, 67, 67, 94, 107, 107, 107, 129, 129, 129, 129, 129, 129, 67, 67, 67, 64, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 94, 94, 107, 129, 129, 129, 129, 129, 129, 129, 129, 67, 67, 67, 67, 67, 67, 37, 37, 1] 129
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 494
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277569 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277569
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277569/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277569
Building REAL300025277570
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277570'
/scratch/stefan/7808390/working/building/REAL300025277570 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277570

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277570/0 /scratch/stefan/7808390/working/building/REAL300025277570 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/450
`/scratch/stefan/7808390/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)(C)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277570 none COC(C)(C)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 187, 201, 201, 130, 130, 130, 105, 62, 62, 62, 62, 62, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 130, 105, 105, 62, 62, 62, 62, 62, 62, 62, 62, 62, 30, 30, 1] 201
rigid atoms, others: [51, 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, 50])
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: REAL300025277570 none COC(C)(C)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 20, 33, 33, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 62, 62, 62, 62, 62, 52, 52, 52, 33, 33, 33, 33, 33, 33, 20, 20, 8, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 62] 201
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277570 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277570
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277570/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277570
Building REAL300025277571
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277571'
/scratch/stefan/7808390/working/building/REAL300025277571 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277571

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277571/0 /scratch/stefan/7808390/working/building/REAL300025277571 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/451
`/scratch/stefan/7808390/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277571 none CC(O)CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 198, 201, 189, 107, 107, 107, 77, 48, 48, 48, 48, 48, 48, 48, 29, 48, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 198, 198, 189, 189, 107, 77, 77, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 29, 1] 603
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])
total number of confs: 1493
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277571 none CC(O)CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [43, 41, 43, 34, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 48, 48, 48, 48, 48, 43, 43, 43, 43, 129, 42, 42, 34, 34, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 48] 603
rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277571 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277571
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277571/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277571
Building REAL300025277572
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277572'
/scratch/stefan/7808390/working/building/REAL300025277572 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277572

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277572/0 /scratch/stefan/7808390/working/building/REAL300025277572 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/452
`/scratch/stefan/7808390/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCS(O)=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.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: REAL300025277572 none CCS(O)=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 14, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 174, 174, 174, 124, 73, 73, 73, 73, 73, 73, 73, 33, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 174, 124, 124, 73, 73, 73, 73, 73, 73, 73, 73, 73, 33, 33, 1] 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])
total number of confs: 793
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277572 none CCS(O)=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 14, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [46, 27, 27, 27, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 15, 73, 73, 73, 73, 73, 46, 46, 46, 46, 46, 27, 27, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 73] 201
rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 302
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277572 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277572
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277572/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277572
Building REAL300025277573
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277573'
/scratch/stefan/7808390/working/building/REAL300025277573 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277573

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277573/0 /scratch/stefan/7808390/working/building/REAL300025277573 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/453
`/scratch/stefan/7808390/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277573 none CN(C)C(=O)CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 126, 126, 126, 91, 49, 49, 49, 49, 49, 49, 49, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 126, 91, 91, 49, 49, 49, 49, 49, 49, 49, 49, 49, 28, 28, 1] 201
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277573 none CN(C)C(=O)CCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 47, 38, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 44, 44, 38, 38, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 49] 201
rigid atoms, others: [48, 45, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277573 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277573
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277573/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277573
Building REAL300025277574
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277574'
/scratch/stefan/7808390/working/building/REAL300025277574 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277574

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277574/0 /scratch/stefan/7808390/working/building/REAL300025277574 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/454
`/scratch/stefan/7808390/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCC(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277574 none C#CCC(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 97, 176, 97, 97, 73, 46, 46, 46, 46, 46, 46, 46, 27, 46, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 176, 176, 176, 176, 97, 73, 73, 46, 46, 46, 46, 46, 46, 46, 46, 46, 27, 27, 1] 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])
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: REAL300025277574 none C#CCC(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [49, 49, 28, 8, 28, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 49, 49, 49, 28, 28, 28, 28, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 46] 201
rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277574 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277574
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277574/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277574
Building REAL300025277575
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277575'
/scratch/stefan/7808390/working/building/REAL300025277575 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277575

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277575/0 /scratch/stefan/7808390/working/building/REAL300025277575 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/455
`/scratch/stefan/7808390/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCO)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277575 none CC(CCO)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [190, 133, 190, 201, 201, 133, 133, 96, 52, 52, 52, 52, 52, 52, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 201, 201, 201, 201, 603, 133, 96, 96, 52, 52, 52, 52, 52, 52, 52, 52, 52, 30, 30, 1] 603
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])
total number of confs: 1508
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: REAL300025277575 none CC(CCO)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [31, 8, 31, 41, 55, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 52, 52, 52, 52, 52, 31, 31, 31, 31, 41, 41, 55, 55, 165, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 52] 603
rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 497
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277575 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277575
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277575/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277575
Building REAL300025277576
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277576'
/scratch/stefan/7808390/working/building/REAL300025277576 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277576

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277576/0 /scratch/stefan/7808390/working/building/REAL300025277576 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/456
`/scratch/stefan/7808390/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C(F)=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277576 none CC1(CNC(=O)C(F)=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 67, 42, 42, 8, 42, 8, 8, 1, 1, 1, 1, 89, 89, 89, 89, 89, 93, 93, 134, 149, 201, 201, 201, 201, 201, 89, 89, 89, 67, 67, 42, 8, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 134, 134, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 663
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: REAL300025277576 none CC1(CNC(=O)C(F)=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 4, 8, 8, 8, 45, 45, 45, 89, 89, 1, 1, 1, 1, 1, 4, 4, 8, 15, 66, 66, 66, 66, 66, 2, 2, 2, 4, 4, 8, 45, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 8, 8, 66] 201
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 353
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277576 none CC1(CNC(=O)C(F)=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [66, 66, 66, 84, 114, 114, 114, 178, 178, 178, 201, 201, 66, 66, 66, 61, 43, 61, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 84, 84, 114, 178, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 43, 43, 1] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 736
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277576 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277576
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277576/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277576
Building REAL300025277577
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277577'
/scratch/stefan/7808390/working/building/REAL300025277577 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277577

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277577/0 /scratch/stefan/7808390/working/building/REAL300025277577 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/457
`/scratch/stefan/7808390/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CC2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277577 none CC1(CNC(=O)CC2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 63, 37, 37, 7, 37, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 84, 84, 132, 150, 201, 201, 201, 201, 201, 83, 83, 83, 63, 63, 37, 7, 7, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 132, 132, 201] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 680
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277577 none CC1(CNC(=O)CC2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 7, 38, 83, 83, 83, 83, 1, 1, 1, 1, 1, 3, 3, 6, 12, 48, 48, 48, 48, 48, 2, 2, 2, 3, 3, 7, 38, 38, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 6, 6, 48] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 12, 13, 14, 15, 16, 45, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
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: REAL300025277577 none CC1(CNC(=O)CC2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 83, 83, 83, 194, 201, 201, 201, 201, 48, 48, 48, 47, 38, 47, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 62, 62, 83, 194, 194, 201, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 48, 38, 38, 1] 201
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])
total number of confs: 787
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277577 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277577
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277577/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277577
Building REAL300025277578
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277578'
/scratch/stefan/7808390/working/building/REAL300025277578 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277578

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277578/0 /scratch/stefan/7808390/working/building/REAL300025277578 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/458
`/scratch/stefan/7808390/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C(F)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277578 none CC1(CNC(=O)C(F)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [78, 67, 50, 50, 20, 50, 6, 20, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 97, 99, 102, 102, 102, 102, 102, 78, 78, 78, 67, 67, 50, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 97, 97, 102] 102
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51])
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: REAL300025277578 none CC1(CNC(=O)C(F)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 6, 6, 6, 28, 28, 58, 78, 78, 78, 1, 1, 1, 1, 1, 2, 2, 5, 7, 21, 21, 21, 21, 21, 2, 2, 2, 3, 3, 6, 28, 61, 61, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 5, 5, 21] 102
rigid atoms, others: [0, 1, 2, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 49, 50, 51])
total number of confs: 368
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: REAL300025277578 none CC1(CNC(=O)C(F)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 23, 35, 35, 35, 70, 70, 89, 102, 102, 102, 21, 21, 21, 21, 16, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 23, 23, 35, 70, 90, 90, 102, 102, 102, 102, 102, 102, 102, 21, 21, 21, 21, 21, 21, 16, 16, 1] 102
rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 437
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277578 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277578
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277578/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277578
Building REAL300025277579
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277579'
/scratch/stefan/7808390/working/building/REAL300025277579 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277579

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277579/0 /scratch/stefan/7808390/working/building/REAL300025277579 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/459
`/scratch/stefan/7808390/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)[C@H](O)CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277579 none CC1(CNC(=O)[C@H](O)CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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: [49, 49, 49, 79, 146, 146, 146, 201, 201, 201, 201, 49, 49, 49, 49, 35, 49, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 79, 79, 146, 603, 201, 201, 49, 49, 49, 49, 49, 49, 35, 35, 1] 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])
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: REAL300025277579 none CC1(CNC(=O)[C@H](O)CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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: [1, 1, 1, 4, 15, 15, 15, 49, 49, 49, 58, 1, 1, 1, 1, 1, 2, 2, 4, 8, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 15, 147, 58, 58, 1, 1, 1, 1, 1, 1, 4, 4, 49] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 11, 12, 34, 14, 13, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 453
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277579 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277579
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277579/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277579
Building REAL300025277580
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277580'
/scratch/stefan/7808390/working/building/REAL300025277580 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277580

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277580/0 /scratch/stefan/7808390/working/building/REAL300025277580 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/460
`/scratch/stefan/7808390/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277580 none CCC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 27, 27, 27, 27, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 57, 57, 57, 57, 57, 27, 43, 43, 43, 43, 43, 27, 27, 27, 27, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 57, 27, 27] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 16, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52])
total number of confs: 227
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277580 none CCC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 27, 27, 27, 27, 27, 27, 29, 29, 62, 93, 201, 201, 201, 201, 201, 1, 4, 4, 4, 3, 3, 2, 2, 2, 1, 8, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 62, 62, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 52, 26, 51] set([0, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277580 none CCC1(C)C=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 133, 133, 133, 98, 57, 57, 57, 57, 57, 57, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 98, 98, 57, 57, 57, 57, 57, 57, 57, 57, 57, 30, 30, 1, 201, 201] 201
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])
total number of confs: 664
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277580 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277580
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277580/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277580
Building REAL300025277581
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277581'
/scratch/stefan/7808390/working/building/REAL300025277581 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277581

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277581/0 /scratch/stefan/7808390/working/building/REAL300025277581 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/461
`/scratch/stefan/7808390/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C)CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025277581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277581 none CCC1(C)CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 39, 39, 39, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 48, 48, 48, 48, 48, 39, 56, 56, 56, 56, 56, 39, 39, 39, 39, 39, 39, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 48, 39, 39] 201
rigid atoms, others: [16, 45, 9, 10, 11, 12, 13, 14, 15, 48, 49, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52, 53, 54])
total number of confs: 280
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277581 none CCC1(C)CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 11, 11, 11, 28, 39, 39, 39, 39, 39, 39, 39, 39, 80, 118, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 11, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 80, 80, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 53, 54, 36, 26, 37] set([0, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277581 none CCC1(C)CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 106, 106, 106, 85, 48, 48, 48, 48, 48, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 85, 85, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 29, 1, 201, 201] 201
rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] 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, 50, 51, 53, 54])
total number of confs: 716
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277581 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277581
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277581/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277581
Building REAL300025277582
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277582'
/scratch/stefan/7808390/working/building/REAL300025277582 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277582

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277582/0 /scratch/stefan/7808390/working/building/REAL300025277582 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/462
`/scratch/stefan/7808390/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1)

`REAL300025277582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277582 none CCN1C=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [53, 21, 21, 21, 21, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 69, 69, 69, 69, 69, 21, 53, 53, 53, 53, 53, 21, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 69] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277582 none CCN1C=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 1, 1, 6, 6, 6, 14, 21, 21, 21, 21, 21, 21, 22, 22, 48, 74, 170, 170, 170, 170, 170, 1, 7, 7, 7, 7, 7, 1, 6, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 48, 48, 170] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 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.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277582 none CCN1C=NC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 170, 170, 170, 170, 140, 140, 140, 106, 69, 69, 69, 69, 69, 69, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 201, 201, 170, 140, 106, 106, 69, 69, 69, 69, 69, 69, 69, 69, 69, 31, 31, 1] 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])
total number of confs: 810
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277582 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277582
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277582/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277582
Building REAL300025277583
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277583'
/scratch/stefan/7808390/working/building/REAL300025277583 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277583

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277583/0 /scratch/stefan/7808390/working/building/REAL300025277583 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/463
`/scratch/stefan/7808390/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)(O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277583 none CCCC(C)(O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 199, 187, 199, 199, 157, 157, 157, 113, 61, 61, 61, 61, 61, 61, 58, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 597, 187, 187, 157, 113, 113, 61, 61, 61, 61, 61, 61, 61, 61, 61, 31, 31, 1] 603
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 1458
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277583 none CCCC(C)(O)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [60, 60, 26, 19, 26, 26, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 61, 61, 61, 61, 61, 60, 60, 60, 60, 60, 60, 60, 26, 26, 26, 78, 19, 19, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 61] 603
rigid atoms, others: [48, 17, 10, 11, 12, 13, 14, 47, 16, 49, 50, 51, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277583 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277583
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277583/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277583
Building REAL300025277584
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277584'
/scratch/stefan/7808390/working/building/REAL300025277584 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277584

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277584/0 /scratch/stefan/7808390/working/building/REAL300025277584 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/464
`/scratch/stefan/7808390/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277584 none CN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [36, 36, 36, 36, 36, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 18, 70, 70, 70, 70, 70, 36, 36, 36, 36, 25, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 11, 70] 201
rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277584 none CN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 16, 36, 36, 36, 36, 36, 36, 40, 40, 82, 128, 201, 201, 201, 201, 201, 2, 2, 2, 1, 4, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 82, 82, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 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])
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: REAL300025277584 none CN1C=NN=C1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 149, 70, 70, 70, 70, 70, 70, 67, 32, 67, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 70, 70, 70, 70, 70, 70, 70, 70, 70, 32, 32, 1] 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])
total number of confs: 752
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277584 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277584
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277584/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277584
Building REAL300025277585
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277585'
/scratch/stefan/7808390/working/building/REAL300025277585 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277585

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277585/0 /scratch/stefan/7808390/working/building/REAL300025277585 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/465
`/scratch/stefan/7808390/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(CC)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277585 none CCCC(CC)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 180, 195, 195, 85, 85, 85, 58, 38, 38, 38, 38, 38, 38, 38, 25, 38, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 180, 180, 85, 58, 58, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 1] 201
rigid atoms, others: [56, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 864
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277585 none CCCC(CC)CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 30, 41, 50, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 56, 56, 56, 56, 56, 56, 56, 42, 50, 49, 50, 50, 50, 30, 30, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 38] 201
rigid atoms, others: [48, 17, 10, 11, 12, 13, 14, 15, 16, 49, 50, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56])
total number of confs: 374
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277585 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277585
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277585/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277585
Building REAL300025277586
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277586'
/scratch/stefan/7808390/working/building/REAL300025277586 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277586

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277586/0 /scratch/stefan/7808390/working/building/REAL300025277586 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/466
`/scratch/stefan/7808390/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CON=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277586 none CC1=CON=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [46, 46, 46, 46, 46, 36, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 58, 58, 58, 58, 58, 46, 46, 46, 46, 36, 36, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 58] 201
rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277586 none CC1=CON=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 18, 18, 18, 31, 46, 46, 46, 46, 46, 46, 46, 46, 75, 113, 201, 201, 201, 201, 201, 2, 2, 2, 1, 7, 7, 18, 31, 31, 46, 46, 46, 46, 46, 46, 46, 46, 46, 75, 75, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30] set([7, 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])
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: REAL300025277586 none CC1=CON=C1CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 148, 148, 148, 89, 58, 58, 58, 58, 58, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 199, 148, 89, 89, 58, 58, 58, 58, 58, 58, 58, 58, 58, 30, 30, 1] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 844
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277586 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277586
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277586/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277586
Building REAL300025277587
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277587'
/scratch/stefan/7808390/working/building/REAL300025277587 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277587

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277587/0 /scratch/stefan/7808390/working/building/REAL300025277587 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/467
`/scratch/stefan/7808390/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1)

`REAL300025277587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277587 none C#CC1=CC=CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 27, 27, 27, 27, 27, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 68, 68, 68, 68, 68, 27, 27, 27, 27, 27, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 68, 27] 201
rigid atoms, others: [43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277587 none C#CC1=CC=CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 5, 5, 19, 27, 27, 27, 27, 27, 27, 31, 31, 71, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 5, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 71, 71, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 47, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 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: REAL300025277587 none C#CC1=CC=CC(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 109, 109, 109, 99, 68, 68, 68, 68, 68, 68, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 109, 99, 99, 68, 68, 68, 68, 68, 68, 68, 68, 68, 30, 30, 1, 201] 201
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
total number of confs: 553
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277587 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277587
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277587/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277587
Building REAL300025277588
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277588'
/scratch/stefan/7808390/working/building/REAL300025277588 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277588

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277588/0 /scratch/stefan/7808390/working/building/REAL300025277588 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/468
`/scratch/stefan/7808390/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(O)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277588 none CC1(CNC(=O)C2(O)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [27, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 28, 28, 50, 60, 77, 77, 77, 77, 77, 27, 27, 27, 18, 18, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 50, 50, 77] 231
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 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])
total number of confs: 280
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277588 none CC1(CNC(=O)C2(O)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 8, 15, 43, 43, 43, 43, 43, 2, 2, 2, 4, 4, 9, 81, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 8, 8, 43] 231
rigid atoms, others: [0, 1, 2, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 50, 51, 52])
total number of confs: 240
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: REAL300025277588 none CC1(CNC(=O)C2(O)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 54, 62, 62, 62, 77, 77, 77, 77, 77, 77, 43, 43, 43, 42, 29, 42, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 54, 54, 62, 231, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 43, 43, 43, 43, 43, 43, 29, 29, 1] 231
rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 516
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277588 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277588
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277588/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277588
Building REAL300025277589
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277589'
/scratch/stefan/7808390/working/building/REAL300025277589 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277589

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277589/0 /scratch/stefan/7808390/working/building/REAL300025277589 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/469
`/scratch/stefan/7808390/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277589 none CC1(CNC(=O)C2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [62, 39, 8, 8, 1, 8, 1, 1, 1, 1, 62, 62, 62, 62, 62, 63, 63, 87, 134, 201, 201, 201, 201, 201, 62, 62, 62, 39, 39, 8, 6, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 87, 87, 201] 603
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 31] set([0, 1, 2, 3, 5, 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])
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: REAL300025277589 none CC1(CNC(=O)C2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [1, 1, 1, 7, 20, 20, 20, 62, 62, 62, 1, 1, 1, 1, 1, 3, 3, 8, 14, 58, 58, 58, 58, 58, 2, 2, 2, 7, 7, 20, 186, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 8, 8, 58] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14] set([3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025277589 none CC1(CNC(=O)C2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [58, 58, 58, 110, 177, 177, 177, 201, 201, 201, 58, 58, 58, 58, 40, 58, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 110, 110, 177, 603, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 40, 40, 1] 603
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])
total number of confs: 1351
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277589 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277589
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277589/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277589
Building REAL300025277590
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277590'
/scratch/stefan/7808390/working/building/REAL300025277590 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277590

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277590/0 /scratch/stefan/7808390/working/building/REAL300025277590 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/470
`/scratch/stefan/7808390/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CS(N)(=O)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277590 none CC1(CNC(=O)CS(N)(=O)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 48, 66, 66, 66, 132, 156, 156, 156, 38, 38, 38, 37, 26, 37, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 48, 48, 66, 132, 132, 156, 156, 38, 38, 38, 38, 38, 38, 26, 26, 1] 156
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])
total number of confs: 678
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: REAL300025277590 none CC1(CNC(=O)CS(N)(=O)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 14, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 33, 86, 86, 86, 1, 1, 1, 1, 1, 4, 4, 7, 12, 38, 38, 38, 38, 38, 2, 2, 2, 3, 3, 7, 33, 33, 86, 86, 1, 1, 1, 1, 1, 1, 7, 7, 38] 156
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 416
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277590 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277590
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277590/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277590
Building REAL300025277591
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277591'
/scratch/stefan/7808390/working/building/REAL300025277591 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277591

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277591/0 /scratch/stefan/7808390/working/building/REAL300025277591 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/471
`/scratch/stefan/7808390/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1)

`REAL300025277591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277591 none CC1=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 36, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 57, 57, 57, 57, 57, 36, 36, 36, 36, 36, 36, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 57, 36] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277591 none CC1=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 9, 9, 9, 27, 36, 36, 36, 36, 36, 36, 38, 38, 81, 122, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 81, 81, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 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])
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: REAL300025277591 none CC1=C(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)C=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 135, 135, 135, 96, 57, 57, 57, 57, 57, 57, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 135, 96, 96, 57, 57, 57, 57, 57, 57, 57, 57, 57, 29, 29, 1, 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])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277591 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277591
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277591/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277591
Building REAL300025277592
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277592'
/scratch/stefan/7808390/working/building/REAL300025277592 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277592

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277592/0 /scratch/stefan/7808390/working/building/REAL300025277592 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/472
`/scratch/stefan/7808390/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CC(=O)[N-]O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277592 none CC1(CNC(=O)C2=CC(=O)[N-]O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [19, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 26, 26, 48, 63, 91, 91, 91, 91, 91, 19, 19, 19, 10, 10, 4, 1, 19, 19, 19, 19, 19, 19, 48, 48, 91] 91
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277592 none CC1(CNC(=O)C2=CC(=O)[N-]O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 16, 16, 16, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 4, 4, 11, 18, 59, 59, 59, 59, 59, 2, 2, 2, 7, 7, 16, 19, 1, 1, 1, 1, 1, 1, 11, 11, 59] 91
rigid atoms, others: [0, 1, 2, 34, 36, 37, 38, 33, 12, 13, 14, 15, 16, 35] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277592 none CC1(CNC(=O)C2=CC(=O)[N-]O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 84, 91, 91, 91, 91, 91, 91, 91, 91, 59, 59, 59, 53, 36, 53, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 84, 84, 91, 91, 59, 59, 59, 59, 59, 59, 36, 36, 1] 91
rigid atoms, others: [41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 345
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277592 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277592
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277592/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277592
Building REAL300025277593
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277593'
/scratch/stefan/7808390/working/building/REAL300025277593 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277593

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277593/0 /scratch/stefan/7808390/working/building/REAL300025277593 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/473
`/scratch/stefan/7808390/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1)

`REAL300025277593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277593 none CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens 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, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 74, 74, 74, 74, 74, 27, 27, 27, 27, 27, 27, 27, 27, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 74, 27, 27, 27, 27] 201
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 195
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: REAL300025277593 none CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens need 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, 6, 6, 6, 17, 27, 27, 27, 27, 27, 27, 30, 30, 72, 109, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 3, 3, 6, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 72, 72, 201, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 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, 45])
total number of confs: 534
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: REAL300025277593 none CCC1(C(=O)NCC2(C)CCCN2C(=O)CSC2=NNC(=O)[N-]2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 145, 145, 145, 115, 74, 74, 74, 74, 74, 74, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 145, 115, 115, 74, 74, 74, 74, 74, 74, 74, 74, 74, 30, 30, 1, 201, 201, 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])
total number of confs: 759
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277593 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277593
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277593/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277593
Building REAL300025277594
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277594'
/scratch/stefan/7808390/working/building/REAL300025277594 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277594

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277594/0 /scratch/stefan/7808390/working/building/REAL300025277594 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/474
`/scratch/stefan/7808390/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277594 none CC1(CNC(=O)C2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [37, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 42, 42, 109, 139, 192, 192, 192, 192, 192, 37, 37, 37, 23, 23, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 109, 109, 192] 192
rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 583
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277594 none CC1(CNC(=O)C2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 13, 13, 13, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 4, 4, 13, 28, 103, 103, 103, 103, 103, 2, 2, 2, 7, 7, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 13, 13, 103] 192
rigid atoms, others: [0, 1, 2, 41, 42, 43, 12, 13, 14, 15, 16, 46, 45, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277594 none CC1(CNC(=O)C2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 145, 165, 165, 165, 192, 192, 192, 192, 192, 103, 103, 103, 97, 40, 97, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 145, 145, 165, 192, 192, 192, 192, 192, 192, 192, 192, 192, 103, 103, 103, 103, 103, 103, 40, 40, 1] 192
rigid atoms, others: [49, 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])
total number of confs: 712
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277594 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277594
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277594/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277594
Building REAL300025277595
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277595'
/scratch/stefan/7808390/working/building/REAL300025277595 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277595

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277595/0 /scratch/stefan/7808390/working/building/REAL300025277595 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/475
`/scratch/stefan/7808390/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277595 none CC1(CNC(=O)C2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [18, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 19, 19, 26, 32, 42, 42, 42, 42, 42, 18, 18, 18, 12, 12, 8, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 26, 26, 42] 42
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025277595 none CC1(CNC(=O)C2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 7, 7, 7, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 8, 15, 33, 33, 33, 33, 33, 2, 2, 2, 4, 4, 7, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 8, 8, 33] 42
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277595 none CC1(CNC(=O)C2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 34, 34, 34, 42, 42, 42, 42, 33, 33, 33, 32, 23, 32, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 34, 42, 42, 42, 42, 33, 33, 33, 33, 33, 33, 23, 23, 1] 42
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])
total number of confs: 131
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277595 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277595
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277595/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277595
Building REAL300025277596
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277596'
/scratch/stefan/7808390/working/building/REAL300025277596 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277596

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277596/0 /scratch/stefan/7808390/working/building/REAL300025277596 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/476
`/scratch/stefan/7808390/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=NOC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277596 none CC1(CNC(=O)C2=NOC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [19, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 7, 1, 19, 19, 19, 19, 19, 19, 19, 26, 26, 34, 34, 34, 34, 34, 19, 19, 19, 16, 16, 9, 7, 7, 21, 1, 19, 19, 19, 19, 19, 19, 26, 26, 34] 102
rigid atoms, others: [4, 6, 7, 8, 9, 10, 12, 36] set([0, 1, 2, 3, 5, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 160
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277596 none CC1(CNC(=O)C2=NOC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 19, 19, 19, 19, 26, 19, 1, 1, 1, 1, 1, 2, 2, 5, 6, 16, 16, 16, 16, 16, 2, 2, 2, 3, 3, 7, 26, 26, 78, 19, 1, 1, 1, 1, 1, 1, 5, 5, 16] 102
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 187
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: REAL300025277596 none CC1(CNC(=O)C2=NOC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 19, 26, 26, 26, 34, 34, 34, 34, 34, 34, 16, 16, 16, 16, 14, 16, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 19, 19, 26, 34, 34, 102, 34, 16, 16, 16, 16, 16, 16, 14, 14, 1] 102
rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 191
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277596 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277596
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277596/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277596
Building REAL300025277597
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277597'
/scratch/stefan/7808390/working/building/REAL300025277597 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277597

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277597/0 /scratch/stefan/7808390/working/building/REAL300025277597 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/477
`/scratch/stefan/7808390/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(C)(C)C)

`REAL300025277597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277597 none CC(=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 142, 142, 142, 92, 56, 56, 56, 56, 56, 56, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 142, 92, 92, 56, 56, 56, 56, 56, 56, 56, 56, 56, 28, 28, 1, 201, 201, 201, 201, 201, 201, 201, 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, 52, 53, 54])
total number of confs: 772
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277597 none CC(=CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 56, 56, 56, 56, 56, 41, 48, 48, 48, 41, 41, 41, 41, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 56, 48, 48, 48, 48, 48, 48, 48, 48, 48] 201
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277597 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277597
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277597/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277597
Building REAL300025277598
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277598'
/scratch/stefan/7808390/working/building/REAL300025277598 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277598

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277598/0 /scratch/stefan/7808390/working/building/REAL300025277598 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/478
`/scratch/stefan/7808390/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277598 none CC1(CNC(=O)C2=CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [33, 24, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 36, 36, 67, 93, 138, 138, 138, 138, 138, 33, 33, 33, 24, 24, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 67, 67, 138] 138
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 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])
total number of confs: 391
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: REAL300025277598 none CC1(CNC(=O)C2=CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 7, 7, 7, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 12, 20, 60, 60, 60, 60, 60, 2, 2, 2, 4, 4, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 12, 12, 60] 138
rigid atoms, others: [0, 1, 2, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 169
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: REAL300025277598 none CC1(CNC(=O)C2=CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [60, 60, 60, 87, 93, 93, 93, 138, 138, 138, 138, 138, 138, 60, 60, 60, 58, 36, 58, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 87, 87, 93, 138, 138, 138, 138, 138, 138, 138, 138, 138, 60, 60, 60, 60, 60, 60, 36, 36, 1] 138
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 445
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277598 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277598
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277598/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277598
Building REAL300025277599
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277599'
/scratch/stefan/7808390/working/building/REAL300025277599 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277599

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277599/0 /scratch/stefan/7808390/working/building/REAL300025277599 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/479
`/scratch/stefan/7808390/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1OCC[C@@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277599 none C[C@@H]1OCC[C@@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [27, 27, 27, 27, 27, 27, 13, 27, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 28, 105, 105, 105, 105, 105, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 15, 15, 105] 201
rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 262
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277599 none C[C@@H]1OCC[C@@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 5, 5, 5, 19, 27, 27, 27, 27, 27, 27, 36, 36, 76, 127, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 76, 76, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 31] set([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, 46, 47, 48, 49])
total number of confs: 539
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277599 none C[C@@H]1OCC[C@@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 195, 201, 195, 195, 145, 105, 105, 105, 105, 105, 105, 83, 33, 83, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 145, 145, 105, 105, 105, 105, 105, 105, 105, 105, 105, 33, 33, 1] 201
rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 713
number of broken/clashed sets: 58
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277599 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277599
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277599/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277599
Building REAL300025277600
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277600'
/scratch/stefan/7808390/working/building/REAL300025277600 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277600

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277600/0 /scratch/stefan/7808390/working/building/REAL300025277600 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/480
`/scratch/stefan/7808390/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277600 none CC1(CNC(=O)C2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [24, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 42, 52, 65, 65, 65, 65, 65, 24, 24, 24, 18, 18, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 42, 42, 65] 65
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277600 none CC1(CNC(=O)C2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 6, 6, 6, 24, 24, 24, 24, 1, 1, 1, 1, 1, 2, 2, 6, 10, 33, 33, 33, 33, 33, 2, 2, 2, 4, 4, 6, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 6, 6, 33] 65
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277600 none CC1(CNC(=O)C2CC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 41, 41, 41, 41, 65, 65, 65, 65, 33, 33, 33, 33, 27, 33, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 41, 41, 41, 65, 65, 65, 65, 65, 65, 33, 33, 33, 33, 33, 33, 27, 27, 1] 65
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])
total number of confs: 241
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277600 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277600
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277600/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277600
Building REAL300025277601
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277601'
/scratch/stefan/7808390/working/building/REAL300025277601 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277601

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277601/0 /scratch/stefan/7808390/working/building/REAL300025277601 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/481
`/scratch/stefan/7808390/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(O)C(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277601 none CCC(O)C(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 188, 201, 134, 188, 134, 134, 95, 60, 60, 60, 60, 60, 60, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 188, 188, 188, 188, 134, 95, 95, 60, 60, 60, 60, 60, 60, 60, 60, 60, 31, 31, 1] 603
rigid atoms, others: [51, 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, 50])
total number of confs: 1489
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277601 none CCC(O)C(C)C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [39, 37, 28, 37, 9, 28, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 60, 60, 60, 60, 60, 39, 39, 39, 39, 39, 37, 111, 28, 28, 28, 28, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 60] 603
rigid atoms, others: [16, 45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 378
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277601 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277601
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277601/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277601
Building REAL300025277602
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277602'
/scratch/stefan/7808390/working/building/REAL300025277602 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277602

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277602/0 /scratch/stefan/7808390/working/building/REAL300025277602 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/482
`/scratch/stefan/7808390/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)OCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277602 none CCC(C)(C)OCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 177, 201, 201, 136, 98, 98, 98, 65, 41, 41, 41, 41, 41, 41, 41, 29, 41, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 98, 65, 65, 41, 41, 41, 41, 41, 41, 41, 41, 41, 29, 29, 1] 201
rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 850
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277602 none CCC(C)(C)OCC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 30, 50, 50, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 41, 41, 41, 41, 41, 65, 65, 65, 65, 65, 50, 50, 50, 50, 50, 50, 14, 14, 6, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 41] 201
rigid atoms, others: [48, 17, 10, 11, 12, 13, 14, 47, 16, 49, 50, 51, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54])
total number of confs: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277602 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277602
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277602/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277602
Building REAL300025277603
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277603'
/scratch/stefan/7808390/working/building/REAL300025277603 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277603

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277603/0 /scratch/stefan/7808390/working/building/REAL300025277603 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/483
`/scratch/stefan/7808390/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CC2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277603 none CC1(CNC(=O)CC2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [82, 63, 35, 35, 7, 35, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 84, 84, 128, 148, 201, 201, 201, 201, 201, 82, 82, 82, 63, 63, 35, 7, 7, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 128, 128, 201] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 673
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277603 none CC1(CNC(=O)CC2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 3, 8, 8, 8, 45, 82, 82, 82, 82, 1, 1, 1, 1, 1, 3, 3, 6, 12, 54, 54, 54, 54, 54, 2, 2, 2, 3, 3, 8, 45, 45, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 6, 6, 54] 201
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 365
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: REAL300025277603 none CC1(CNC(=O)CC2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [54, 54, 54, 68, 93, 93, 93, 176, 201, 201, 201, 201, 54, 54, 54, 51, 34, 51, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 68, 68, 93, 176, 176, 201, 201, 201, 201, 54, 54, 54, 54, 54, 54, 34, 34, 1] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 817
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277603 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277603
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277603/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277603
Building REAL300025277604
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277604'
/scratch/stefan/7808390/working/building/REAL300025277604 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277604

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277604/0 /scratch/stefan/7808390/working/building/REAL300025277604 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/484
`/scratch/stefan/7808390/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277604 none CC1(CNC(=O)C(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [33, 27, 17, 17, 6, 17, 1, 6, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 49, 51, 53, 53, 53, 53, 53, 33, 33, 33, 27, 27, 17, 6, 18, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 49, 49, 53] 159
rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 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])
total number of confs: 238
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277604 none CC1(CNC(=O)C(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 7, 7, 7, 23, 23, 33, 33, 33, 1, 1, 1, 1, 1, 2, 2, 5, 7, 21, 21, 21, 21, 21, 2, 2, 2, 3, 3, 7, 23, 69, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 5, 5, 21] 159
rigid atoms, others: [0, 1, 2, 41, 42, 43, 12, 13, 14, 15, 16, 46, 45, 44] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 234
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277604 none CC1(CNC(=O)C(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 23, 30, 30, 30, 41, 41, 53, 53, 53, 21, 21, 21, 21, 18, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 23, 23, 30, 41, 123, 53, 53, 53, 53, 53, 53, 53, 21, 21, 21, 21, 21, 21, 18, 18, 1] 159
rigid atoms, others: [49, 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])
total number of confs: 330
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277604 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277604
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277604/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277604
Building REAL300025277605
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277605'
/scratch/stefan/7808390/working/building/REAL300025277605 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277605

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277605/0 /scratch/stefan/7808390/working/building/REAL300025277605 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/485
`/scratch/stefan/7808390/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=NNC(=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277605 none CC1(CNC(=O)C2=NNC(=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [43, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 46, 46, 79, 95, 116, 116, 116, 116, 116, 43, 43, 43, 29, 29, 10, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 79, 79, 116] 116
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277605 none CC1(CNC(=O)C2=NNC(=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 11, 11, 11, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 4, 4, 10, 17, 62, 62, 62, 62, 62, 2, 2, 2, 5, 5, 11, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 10, 10, 62] 116
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277605 none CC1(CNC(=O)C2=NNC(=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 89, 102, 102, 102, 116, 116, 116, 116, 116, 116, 62, 62, 62, 59, 36, 59, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 89, 89, 102, 116, 116, 116, 116, 116, 62, 62, 62, 62, 62, 62, 36, 36, 1] 116
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 425
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277605 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277605
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277605/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277605
Building REAL300025277606
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277606'
/scratch/stefan/7808390/working/building/REAL300025277606 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277606

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277606/0 /scratch/stefan/7808390/working/building/REAL300025277606 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/486
`/scratch/stefan/7808390/working/3D/486' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCCNC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277606 none CC1(CNC(=O)CCCNC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 72, 72, 72, 168, 188, 198, 201, 201, 201, 39, 39, 39, 39, 31, 39, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 50, 50, 72, 168, 168, 191, 191, 197, 196, 201, 201, 201, 39, 39, 39, 39, 39, 39, 31, 31, 1] 201
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 899
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: REAL300025277606 none CC1(CNC(=O)CCCNC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 7, 42, 56, 80, 140, 140, 140, 1, 1, 1, 1, 1, 2, 2, 5, 10, 39, 39, 39, 39, 39, 2, 2, 2, 3, 3, 7, 42, 42, 65, 65, 76, 75, 140, 140, 140, 1, 1, 1, 1, 1, 1, 5, 5, 39] 201
rigid atoms, others: [0, 1, 2, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 663
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277606 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277606
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277606/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277606
Building REAL300025277607
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277607'
/scratch/stefan/7808390/working/building/REAL300025277607 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277607

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277607/0 /scratch/stefan/7808390/working/building/REAL300025277607 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/487
`/scratch/stefan/7808390/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CC=NO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277607 none CC1(CNC(=O)C2=CC=NO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [31, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 39, 39, 85, 123, 180, 180, 180, 180, 180, 31, 31, 31, 17, 17, 6, 1, 1, 31, 31, 31, 31, 31, 31, 85, 85, 180] 180
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 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: REAL300025277607 none CC1(CNC(=O)C2=CC=NO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 16, 16, 16, 31, 31, 31, 31, 1, 1, 1, 1, 1, 4, 4, 14, 33, 108, 108, 108, 108, 108, 2, 2, 2, 7, 7, 16, 31, 31, 1, 1, 1, 1, 1, 1, 14, 14, 108] 180
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 11, 12, 34, 14, 13, 15] set([3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277607 none CC1(CNC(=O)C2=CC=NO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 153, 161, 161, 161, 180, 180, 180, 180, 108, 108, 108, 102, 39, 102, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 153, 153, 161, 180, 180, 108, 108, 108, 108, 108, 108, 39, 39, 1] 180
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])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277607 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277607
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277607/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277607
Building REAL300025277608
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277608'
/scratch/stefan/7808390/working/building/REAL300025277608 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277608

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277608/0 /scratch/stefan/7808390/working/building/REAL300025277608 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/488
`/scratch/stefan/7808390/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C23CCC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277608 none CC1(CNC(=O)C23CCC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [20, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 21, 21, 51, 72, 110, 110, 110, 110, 110, 20, 20, 20, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 51, 51, 110] 110
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 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])
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: REAL300025277608 none CC1(CNC(=O)C23CCC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 6, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 3, 3, 10, 17, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 10, 10, 48] 110
rigid atoms, others: [0, 1, 2, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277608 none CC1(CNC(=O)C23CCC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [48, 48, 48, 67, 69, 69, 69, 110, 110, 110, 110, 110, 110, 48, 48, 48, 47, 31, 47, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 67, 67, 69, 110, 110, 110, 110, 110, 110, 110, 110, 110, 48, 48, 48, 48, 48, 48, 31, 31, 1] 110
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 339
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277608 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277608
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277608/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277608
Building REAL300025277609
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277609'
/scratch/stefan/7808390/working/building/REAL300025277609 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277609

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277609/0 /scratch/stefan/7808390/working/building/REAL300025277609 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/489
`/scratch/stefan/7808390/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CC23CC(O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277609 none CC1(CNC(=O)C2CC23CC(O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
396  conformations in input
total number of sets (complete confs): 396
using faster count positions algorithm for large data
unique positions, atoms: [34, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 35, 35, 68, 92, 132, 132, 132, 132, 132, 34, 34, 34, 25, 25, 10, 1, 1, 1, 1, 1, 1, 6, 1, 1, 34, 34, 34, 34, 34, 34, 68, 68, 132] 396
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 409
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: REAL300025277609 none CC1(CNC(=O)C2CC23CC(O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
396  conformations in input
total number of sets (complete confs): 396
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 8, 8, 8, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 3, 3, 7, 13, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 8, 34, 34, 34, 34, 34, 34, 102, 34, 34, 1, 1, 1, 1, 1, 1, 7, 7, 50] 396
rigid atoms, others: [0, 1, 2, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 278
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: REAL300025277609 none CC1(CNC(=O)C2CC23CC(O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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
396  conformations in input
total number of sets (complete confs): 396
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 79, 85, 85, 85, 132, 132, 132, 132, 132, 132, 50, 50, 50, 49, 34, 49, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 79, 79, 85, 132, 132, 132, 132, 132, 132, 396, 132, 132, 50, 50, 50, 50, 50, 50, 34, 34, 1] 396
rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 913
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277609 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277609
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277609/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277609
Building REAL300025277610
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277610'
/scratch/stefan/7808390/working/building/REAL300025277610 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277610

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277610/0 /scratch/stefan/7808390/working/building/REAL300025277610 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/490
`/scratch/stefan/7808390/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C=CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277610 none CC1(CNC(=O)C=CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 50, 33, 33, 8, 32, 8, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 100, 124, 201, 201, 201, 201, 201, 67, 67, 67, 50, 50, 33, 9, 8, 1, 1, 1, 67, 67, 67, 67, 67, 67, 100, 100, 201] 201
rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277610 none CC1(CNC(=O)C=CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 32, 32, 67, 67, 67, 67, 1, 1, 1, 1, 1, 2, 2, 7, 12, 57, 57, 57, 57, 57, 2, 2, 2, 4, 4, 7, 33, 33, 67, 67, 67, 1, 1, 1, 1, 1, 1, 7, 7, 57] 201
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277610 none CC1(CNC(=O)C=CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [57, 57, 57, 91, 113, 113, 113, 170, 170, 201, 201, 201, 201, 57, 57, 57, 57, 40, 57, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 91, 91, 113, 170, 170, 201, 201, 201, 57, 57, 57, 57, 57, 57, 40, 40, 1] 201
rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 730
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277610 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277610
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277610/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277610
Building REAL300025277611
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277611'
/scratch/stefan/7808390/working/building/REAL300025277611 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277611

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277611/0 /scratch/stefan/7808390/working/building/REAL300025277611 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/491
`/scratch/stefan/7808390/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(F)F)

`REAL300025277611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277611 none CC(CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 124, 124, 124, 96, 50, 50, 50, 50, 50, 50, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 199, 124, 96, 96, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 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])
total number of confs: 874
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277611 none CC(CC(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)C(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 50, 50, 50, 50, 50, 51, 53, 53, 51, 51, 51, 51, 38, 38, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 53] 201
rigid atoms, others: [11, 38, 6, 7, 8, 9, 10, 39, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277611 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277611
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277611/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277611
Building REAL300025277612
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277612'
/scratch/stefan/7808390/working/building/REAL300025277612 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277612

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277612/0 /scratch/stefan/7808390/working/building/REAL300025277612 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/492
`/scratch/stefan/7808390/working/3D/492' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C[C@@H]2CCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277612 none CC1(CNC(=O)C[C@@H]2CCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 44, 25, 25, 7, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 68, 68, 106, 130, 201, 201, 201, 201, 201, 65, 65, 65, 44, 44, 25, 7, 7, 1, 1, 1, 1, 1, 1, 3, 65, 65, 65, 65, 65, 65, 106, 106, 201] 603
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 615
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277612 none CC1(CNC(=O)C[C@@H]2CCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 3, 7, 7, 7, 33, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 3, 3, 8, 16, 59, 59, 59, 59, 59, 2, 2, 2, 3, 3, 7, 33, 33, 65, 65, 65, 65, 65, 65, 195, 1, 1, 1, 1, 1, 1, 8, 8, 59] 603
rigid atoms, others: [0, 1, 2, 49, 48, 44, 45, 46, 15, 16, 17, 18, 19, 47] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52])
total number of confs: 513
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277612 none CC1(CNC(=O)C[C@@H]2CCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [59, 59, 59, 79, 101, 101, 101, 193, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 56, 41, 56, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 79, 79, 101, 193, 193, 201, 201, 201, 201, 201, 201, 603, 59, 59, 59, 59, 59, 59, 41, 41, 1] 603
rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 1460
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277612 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277612
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277612/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277612
Building REAL300025277613
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277613'
/scratch/stefan/7808390/working/building/REAL300025277613 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277613

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277613/0 /scratch/stefan/7808390/working/building/REAL300025277613 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/493
`/scratch/stefan/7808390/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CC=CC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277613 none C[C@@H]1CC=CC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 26, 11, 26, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 20, 82, 82, 82, 82, 82, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 11, 82] 201
rigid atoms, others: [48, 45, 49, 44, 12, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52])
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: REAL300025277613 none C[C@@H]1CC=CC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 16, 26, 26, 26, 26, 26, 26, 34, 34, 77, 126, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 77, 77, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 7, 8, 9, 34, 35, 32, 36, 37, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277613 none C[C@@H]1CC=CC[C@H]1C(=O)NCC1(C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 168, 201, 168, 168, 124, 82, 82, 82, 82, 82, 82, 68, 30, 68, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 124, 124, 82, 82, 82, 82, 82, 82, 82, 82, 82, 30, 30, 1] 201
rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277613 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277613
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277613/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277613
Building REAL300025277614
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277614'
/scratch/stefan/7808390/working/building/REAL300025277614 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277614

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277614/0 /scratch/stefan/7808390/working/building/REAL300025277614 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/494
`/scratch/stefan/7808390/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(NC(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025277614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277614 none CC1(CNC(=O)C2(NC(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [7, 6, 5, 5, 1, 5, 1, 1, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 10, 11, 15, 15, 15, 15, 15, 7, 7, 7, 6, 6, 5, 3, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 10, 10, 15] 15
rigid atoms, others: [4, 37, 6, 7, 11, 12, 36, 38, 39] set([0, 1, 2, 3, 5, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 54
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277614 none CC1(CNC(=O)C2(NC(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
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, 3, 4, 4, 4, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 5, 7, 15, 15, 15, 15, 15, 2, 2, 2, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 15] 15
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277614 none CC1(CNC(=O)C2(NC(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 36
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277614 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277614
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277614/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277614
Building REAL300025277615
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277615'
/scratch/stefan/7808390/working/building/REAL300025277615 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277615

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277615/0 /scratch/stefan/7808390/working/building/REAL300025277615 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/495
`/scratch/stefan/7808390/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277615 none CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 86, 86, 86, 86, 86, 60, 47, 60, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 145, 86, 86, 86, 86, 86, 86, 47, 47, 1, 86, 86, 86] 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])
total number of confs: 793
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277615 none CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 18, 86, 86, 86, 86, 86, 1, 1, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 10, 10, 86, 1, 1, 1] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 39, 37, 20, 21, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 34, 35, 36])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277615 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277615
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277615/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277615
Building REAL300025277616
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277616'
/scratch/stefan/7808390/working/building/REAL300025277616 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277616

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277616/0 /scratch/stefan/7808390/working/building/REAL300025277616 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/496
`/scratch/stefan/7808390/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277616 none COCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 108, 108, 108, 49, 49, 49, 49, 49, 32, 25, 32, 12, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 201, 108, 49, 49, 49, 49, 49, 49, 25, 25, 1, 49, 49, 49] 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])
total number of confs: 758
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277616 none COCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [40, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 49, 49, 49, 49, 49, 1, 1, 40, 40, 40, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 5, 5, 49, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277616 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277616
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277616/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277616
Building REAL300025277617
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277617'
/scratch/stefan/7808390/working/building/REAL300025277617 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277617

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277617/0 /scratch/stefan/7808390/working/building/REAL300025277617 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/497
`/scratch/stefan/7808390/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277617 none CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 11, 8, 5, 5, 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, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 154, 154, 154, 154, 154, 100, 57, 100, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 201, 201, 201, 201, 154, 154, 154, 154, 154, 154, 57, 57, 1, 154, 154, 154] 201
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])
total number of confs: 610
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277617 none CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 11, 8, 5, 5, 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, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 50, 154, 154, 154, 154, 154, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 22, 22, 154, 1, 1, 1] 201
rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 8, 9, 19, 20, 25, 26, 27, 28, 29, 30, 36] set([0, 1, 2, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277617 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277617
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277617/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277617
Building REAL300025277618
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277618'
/scratch/stefan/7808390/working/building/REAL300025277618 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277618

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277618/0 /scratch/stefan/7808390/working/building/REAL300025277618 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/498
`/scratch/stefan/7808390/working/3D/498' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3)C2C1)

`REAL300025277618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277618 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 15, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 1, 1, 10, 10, 78, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 1, 1, 1] 201
rigid atoms, others: [1, 38, 39, 40, 10, 11, 12, 13, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277618 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 45, 13, 1, 1, 1, 1, 1, 1, 1, 56, 78, 78, 78, 78, 78, 134, 134, 134, 201, 201, 78, 78, 45, 45, 1, 78, 78, 78, 78, 78, 78, 134, 201, 201, 201, 201, 201, 78, 78, 78] 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: 692
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277618 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 29, 42, 83, 121, 201, 201, 201, 201, 201, 29, 29, 29, 29, 10, 10, 1, 10, 1, 1, 1, 29, 29, 83, 83, 201, 29, 29, 29, 29, 29, 29, 10, 1, 1, 1, 1, 1, 29, 29, 29] 201
rigid atoms, others: [33, 34, 35, 36, 37, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 533
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277618 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277618
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277618/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277618
Building REAL300025277619
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277619'
/scratch/stefan/7808390/working/building/REAL300025277619 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277619

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277619/0 /scratch/stefan/7808390/working/building/REAL300025277619 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/499
`/scratch/stefan/7808390/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3)C2C1)

`REAL300025277619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277619 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 8, 12, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 1, 1, 8, 8, 54, 1, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1] 201
rigid atoms, others: [32, 1, 43, 41, 10, 11, 12, 13, 14, 15, 42, 22, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 139
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277619 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 28, 12, 1, 1, 1, 1, 1, 1, 1, 38, 54, 54, 54, 54, 54, 90, 90, 90, 201, 201, 201, 54, 54, 28, 28, 1, 54, 54, 54, 54, 54, 54, 90, 201, 201, 201, 201, 201, 201, 201, 54, 54, 54] 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: 624
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: REAL300025277619 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 22, 34, 67, 104, 201, 201, 201, 201, 201, 22, 22, 22, 22, 9, 9, 1, 9, 1, 1, 1, 1, 22, 22, 67, 67, 201, 22, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43])
total number of confs: 507
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277619 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277619
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277619/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277619
Building REAL300025277620
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277620'
/scratch/stefan/7808390/working/building/REAL300025277620 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277620

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277620/0 /scratch/stefan/7808390/working/building/REAL300025277620 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/500
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CCCC3)C2C1)

`REAL300025277620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277620 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 13, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 1, 1, 8, 8, 47, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1] 201
rigid atoms, others: [32, 1, 45, 33, 44, 10, 11, 12, 13, 14, 15, 46, 23, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277620 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 35, 47, 47, 47, 47, 47, 102, 102, 102, 201, 201, 201, 201, 47, 47, 30, 30, 1, 47, 47, 47, 47, 47, 47, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 47, 47, 47] 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: 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: REAL300025277620 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 30, 38, 70, 110, 201, 201, 201, 201, 201, 30, 30, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 30, 30, 70, 70, 201, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46])
total number of confs: 496
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277620 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277620
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277620/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277620
Building REAL300025277621
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277621'
/scratch/stefan/7808390/working/building/REAL300025277621 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277621

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277621/0 /scratch/stefan/7808390/working/building/REAL300025277621 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/501
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CCOCC3)C2C1)

`REAL300025277621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277621 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 14, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 1, 1, 9, 9, 52, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 148
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277621 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 36, 52, 52, 52, 52, 52, 113, 113, 113, 201, 201, 201, 201, 201, 52, 52, 30, 30, 1, 52, 52, 52, 52, 52, 52, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 52, 52] 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: 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: REAL300025277621 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 24, 35, 74, 114, 201, 201, 201, 201, 201, 24, 24, 24, 24, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 74, 74, 201, 24, 24, 24, 24, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 35, 45, 46, 47])
total number of confs: 518
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277621 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277621
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277621/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277621
Building REAL300025277622
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277622'
/scratch/stefan/7808390/working/building/REAL300025277622 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277622

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277622/0 /scratch/stefan/7808390/working/building/REAL300025277622 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/502
`/scratch/stefan/7808390/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277622 none O=C(CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 32, 46, 46, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 10, 40, 40, 40, 40, 40, 1, 1, 32, 32, 46, 46, 46, 46, 46, 6, 1, 1, 1, 1, 1, 1, 7, 7, 40, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
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: REAL300025277622 none O=C(CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 1, 1, 1, 1, 15, 15, 46, 46, 46, 46, 46, 54, 54, 87, 125, 201, 201, 201, 201, 201, 46, 46, 3, 3, 1, 1, 1, 1, 1, 15, 46, 46, 46, 46, 46, 46, 87, 87, 201, 46, 46, 46] 201
rigid atoms, others: [2, 3, 4, 5, 26, 27, 28, 29, 30] set([0, 1, 6, 7, 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: 542
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277622 none O=C(CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 157, 201, 201, 40, 40, 40, 40, 40, 30, 27, 30, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 157, 157, 201, 201, 201, 201, 201, 88, 40, 40, 40, 40, 40, 40, 27, 27, 1, 40, 40, 40] 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])
total number of confs: 816
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277622 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277622
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277622/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277622
Building REAL300025277623
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277623'
/scratch/stefan/7808390/working/building/REAL300025277623 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277623

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277623/0 /scratch/stefan/7808390/working/building/REAL300025277623 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/503
`/scratch/stefan/7808390/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277623 none CC(C)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 200, 201, 201, 200, 200, 87, 87, 87, 87, 87, 56, 47, 56, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 200, 87, 87, 87, 87, 87, 87, 47, 47, 1, 87, 87, 87] 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])
total number of confs: 608
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277623 none CC(C)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 19, 87, 87, 87, 87, 87, 1, 1, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 9, 9, 87, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277623 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277623
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277623/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277623
Building REAL300025277624
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277624'
/scratch/stefan/7808390/working/building/REAL300025277624 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277624

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277624/0 /scratch/stefan/7808390/working/building/REAL300025277624 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/504
`/scratch/stefan/7808390/working/3D/504' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277624 none CC(F)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 15, 15, 1, 11, 8, 5, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 165, 201, 201, 165, 165, 75, 75, 75, 75, 75, 49, 42, 49, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 165, 75, 75, 75, 75, 75, 75, 42, 42, 1, 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])
total number of confs: 707
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277624 none CC(F)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 15, 15, 1, 11, 8, 5, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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: [31, 6, 31, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 75, 75, 75, 75, 75, 1, 1, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 9, 9, 75, 1, 1, 1] 201
rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 39, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 34, 35, 36])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277624 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277624
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277624/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277624
Building REAL300025277625
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277625'
/scratch/stefan/7808390/working/building/REAL300025277625 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277625

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277625/0 /scratch/stefan/7808390/working/building/REAL300025277625 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/505
`/scratch/stefan/7808390/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277625 none COCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 166, 166, 166, 77, 77, 77, 77, 77, 47, 38, 47, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 166, 77, 77, 77, 77, 77, 77, 38, 38, 1, 77, 77, 77] 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])
total number of confs: 711
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277625 none COCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 77, 77, 77, 77, 77, 1, 1, 27, 27, 27, 25, 25, 6, 1, 1, 1, 1, 1, 1, 6, 6, 77, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 39, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 35, 36, 37])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277625 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277625
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277625/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277625
Building REAL300025277626
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277626'
/scratch/stefan/7808390/working/building/REAL300025277626 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277626

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277626/0 /scratch/stefan/7808390/working/building/REAL300025277626 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/506
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=CC=N3)C2C1)

`REAL300025277626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277626 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 35, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 17, 17, 119, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277626 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 13, 1, 1, 1, 1, 1, 1, 1, 78, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 48, 48, 1, 119, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 119, 119, 119] 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: 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: REAL300025277626 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 67, 116, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 67, 67, 201, 10, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [36, 37, 38, 39, 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, 35, 40, 41, 42])
total number of confs: 471
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277626 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277626
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277626/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277626
Building REAL300025277627
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277627'
/scratch/stefan/7808390/working/building/REAL300025277627 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277627

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277627/0 /scratch/stefan/7808390/working/building/REAL300025277627 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/507
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=NC=C3)C2C1)

`REAL300025277627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277627 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 31, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 6, 10, 10, 1, 1, 14, 14, 106, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277627 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 13, 1, 1, 1, 1, 1, 1, 1, 70, 106, 106, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 44, 44, 1, 106, 106, 106, 106, 106, 106, 201, 201, 201, 201, 201, 106, 106, 106] 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: 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: REAL300025277627 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 27, 69, 124, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 69, 69, 201, 10, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [36, 37, 38, 39, 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, 35, 40, 41, 42])
total number of confs: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277627 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277627
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277627/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277627
Building REAL300025277628
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277628'
/scratch/stefan/7808390/working/building/REAL300025277628 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277628

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277628/0 /scratch/stefan/7808390/working/building/REAL300025277628 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/508
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=C(F)C=C3)C2C1)

`REAL300025277628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277628 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 31, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 1, 1, 15, 15, 105, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277628 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 13, 1, 1, 1, 1, 1, 1, 1, 70, 105, 105, 105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 44, 44, 1, 105, 105, 105, 105, 105, 105, 201, 201, 201, 201, 201, 105, 105, 105] 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: 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: REAL300025277628 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 28, 68, 126, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 68, 68, 201, 10, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 479
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277628 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277628
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277628/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277628
Building REAL300025277629
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277629'
/scratch/stefan/7808390/working/building/REAL300025277629 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277629

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277629/0 /scratch/stefan/7808390/working/building/REAL300025277629 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/509
`/scratch/stefan/7808390/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277629 none CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 199, 110, 110, 110, 54, 54, 54, 54, 54, 39, 34, 39, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 199, 199, 110, 54, 54, 54, 54, 54, 54, 34, 34, 1, 54, 54, 54] 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])
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: REAL300025277629 none CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 54, 54, 54, 54, 54, 1, 1, 46, 46, 46, 46, 46, 37, 37, 6, 1, 1, 1, 1, 1, 1, 7, 7, 54, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277629 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277629
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277629/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277629
Building REAL300025277630
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277630'
/scratch/stefan/7808390/working/building/REAL300025277630 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277630

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277630/0 /scratch/stefan/7808390/working/building/REAL300025277630 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/510
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=CN=C3)C2C1)

`REAL300025277630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277630 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [4, 1, 4, 16, 31, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 16, 16, 105, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39])
total number of confs: 199
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: REAL300025277630 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [77, 47, 13, 1, 1, 1, 1, 1, 1, 1, 77, 105, 105, 105, 105, 105, 166, 166, 166, 201, 201, 201, 201, 201, 105, 105, 47, 47, 1, 105, 105, 105, 105, 105, 105, 166, 201, 201, 201, 201, 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: 584
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: REAL300025277630 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [27, 16, 27, 64, 106, 201, 201, 201, 201, 201, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 64, 64, 201, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 16, 16, 16] 201
rigid atoms, others: [36, 37, 38, 39, 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, 35, 40, 41, 42])
total number of confs: 477
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277630 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277630
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277630/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277630
Building REAL300025277631
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277631'
/scratch/stefan/7808390/working/building/REAL300025277631 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277631

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277631/0 /scratch/stefan/7808390/working/building/REAL300025277631 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/511
`/scratch/stefan/7808390/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277631 none O=C(CC1=CC=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 14, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 29, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 49, 49, 49, 49, 49, 1, 1, 29, 29, 41, 41, 41, 6, 1, 1, 1, 1, 1, 1, 5, 5, 49, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277631 none O=C(CC1=CC=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 14, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 15, 15, 41, 41, 41, 41, 41, 51, 51, 75, 113, 201, 201, 201, 201, 201, 41, 41, 2, 2, 1, 1, 1, 15, 41, 41, 41, 41, 41, 41, 75, 75, 201, 41, 41, 41] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025277631 none O=C(CC1=CC=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 14, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [120, 120, 120, 184, 201, 201, 201, 201, 49, 49, 49, 49, 49, 32, 27, 32, 12, 1, 1, 1, 1, 1, 1, 1, 49, 49, 184, 184, 201, 201, 201, 120, 49, 49, 49, 49, 49, 49, 27, 27, 1, 49, 49, 49] 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])
total number of confs: 737
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277631 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277631
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277631/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277631
Building REAL300025277632
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277632'
/scratch/stefan/7808390/working/building/REAL300025277632 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277632

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277632/0 /scratch/stefan/7808390/working/building/REAL300025277632 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/512
`/scratch/stefan/7808390/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CO3)C2C1)

`REAL300025277632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277632 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 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, 7, 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: [4, 1, 4, 20, 39, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 1, 1, 20, 20, 126, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
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: REAL300025277632 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 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, 7, 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: [82, 46, 13, 1, 1, 1, 1, 1, 1, 1, 82, 126, 126, 126, 126, 126, 194, 194, 194, 201, 201, 201, 201, 126, 126, 46, 46, 1, 126, 126, 126, 126, 126, 126, 194, 201, 201, 201, 126, 126, 126] 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: 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: REAL300025277632 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 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, 7, 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: [23, 14, 23, 71, 119, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 14, 14, 71, 71, 201, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 472
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277632 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277632
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277632/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277632
Building REAL300025277633
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277633'
/scratch/stefan/7808390/working/building/REAL300025277633 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277633

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277633/0 /scratch/stefan/7808390/working/building/REAL300025277633 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/513
`/scratch/stefan/7808390/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277633 none CC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 89, 89, 89, 40, 40, 40, 40, 40, 28, 24, 28, 11, 1, 1, 1, 1, 1, 1, 1, 40, 40, 201, 201, 201, 201, 201, 201, 89, 40, 40, 40, 40, 40, 40, 24, 24, 1, 40, 40, 40] 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])
total number of confs: 778
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277633 none CC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [44, 44, 44, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 40, 40, 40, 40, 40, 1, 1, 44, 44, 44, 44, 40, 40, 6, 1, 1, 1, 1, 1, 1, 5, 5, 40, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277633 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277633
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277633/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277633
Building REAL300025277634
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277634'
/scratch/stefan/7808390/working/building/REAL300025277634 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277634

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277634/0 /scratch/stefan/7808390/working/building/REAL300025277634 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/514
`/scratch/stefan/7808390/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=C1)

`REAL300025277634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277634 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 18, 69, 69, 69, 69, 69, 1, 1, 21, 21, 21, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 10, 10, 69, 1, 1, 1, 21, 21] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43])
total number of confs: 140
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277634 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 33, 33, 67, 106, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 21, 67, 67, 201, 21, 21, 21, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 43, 23, 24, 25] set([4, 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])
total number of confs: 502
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: REAL300025277634 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 121, 121, 121, 69, 69, 69, 69, 69, 46, 31, 46, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 121, 69, 69, 69, 69, 69, 69, 31, 31, 1, 69, 69, 69, 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])
total number of confs: 512
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277634 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277634
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277634/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277634
Building REAL300025277635
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277635'
/scratch/stefan/7808390/working/building/REAL300025277635 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277635

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277635/0 /scratch/stefan/7808390/working/building/REAL300025277635 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/515
`/scratch/stefan/7808390/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1)

`REAL300025277635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277635 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 43, 123, 123, 123, 123, 123, 1, 1, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 25, 25, 123, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
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: REAL300025277635 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 21, 21, 21, 21, 21, 45, 45, 108, 144, 201, 201, 201, 201, 201, 21, 21, 1, 2, 2, 2, 1, 1, 7, 21, 21, 21, 21, 21, 21, 108, 108, 201, 21, 21, 21] 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])
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: REAL300025277635 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 197, 197, 197, 123, 123, 123, 123, 123, 77, 43, 77, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 201, 197, 123, 123, 123, 123, 123, 123, 43, 43, 1, 123, 123, 123] 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])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277635 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277635
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277635/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277635
Building REAL300025277636
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277636'
/scratch/stefan/7808390/working/building/REAL300025277636 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277636

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277636/0 /scratch/stefan/7808390/working/building/REAL300025277636 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/516
`/scratch/stefan/7808390/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277636 none O=C(C=CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 34, 34, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 74, 74, 74, 74, 74, 1, 1, 34, 34, 39, 39, 39, 6, 1, 1, 1, 1, 1, 1, 9, 9, 74, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 44, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 39, 40, 41])
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: REAL300025277636 none O=C(C=CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 1, 1, 16, 16, 39, 39, 39, 39, 39, 52, 52, 78, 125, 201, 201, 201, 201, 201, 39, 39, 4, 3, 1, 1, 1, 16, 39, 39, 39, 39, 39, 39, 78, 78, 201, 39, 39, 39] 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, 43, 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: REAL300025277636 none O=C(C=CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [154, 154, 154, 201, 201, 201, 201, 201, 201, 74, 74, 74, 74, 74, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 154, 74, 74, 74, 74, 74, 74, 29, 29, 1, 74, 74, 74] 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])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277636 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277636
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277636/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277636
Building REAL300025277637
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277637'
/scratch/stefan/7808390/working/building/REAL300025277637 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277637

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277637/0 /scratch/stefan/7808390/working/building/REAL300025277637 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/517
`/scratch/stefan/7808390/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3F)C2C1)

`REAL300025277637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277637 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 23, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 8, 17, 17, 17, 1, 1, 11, 11, 95, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277637 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 62, 95, 95, 95, 95, 95, 194, 194, 194, 201, 201, 197, 201, 201, 201, 95, 95, 42, 42, 1, 95, 95, 95, 95, 95, 95, 194, 201, 201, 201, 201, 95, 95, 95] 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: 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: REAL300025277637 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 17, 27, 66, 110, 201, 201, 201, 201, 201, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 17, 17, 66, 66, 201, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 478
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277637 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277637
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277637/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277637
Building REAL300025277638
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277638'
/scratch/stefan/7808390/working/building/REAL300025277638 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277638

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277638/0 /scratch/stefan/7808390/working/building/REAL300025277638 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/518
`/scratch/stefan/7808390/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3)C2C1)

`REAL300025277638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277638 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 15, 31, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 6, 11, 11, 1, 1, 15, 15, 103, 1, 1, 1, 1, 1, 1, 6, 11, 11, 6, 11, 11, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40])
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: REAL300025277638 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 42, 13, 1, 1, 1, 1, 1, 1, 1, 67, 103, 103, 103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 42, 42, 1, 103, 103, 103, 103, 103, 103, 201, 201, 201, 201, 201, 201, 103, 103, 103] 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: 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: REAL300025277638 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 11, 29, 68, 122, 201, 201, 201, 201, 201, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 68, 68, 201, 11, 11, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42, 43])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277638 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277638
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277638/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277638
Building REAL300025277639
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277639'
/scratch/stefan/7808390/working/building/REAL300025277639 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277639

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277639/0 /scratch/stefan/7808390/working/building/REAL300025277639 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/519
`/scratch/stefan/7808390/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277639 none CC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 124, 124, 124, 54, 54, 54, 54, 54, 40, 33, 40, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 54, 54, 54, 54, 54, 54, 33, 33, 1, 54, 54, 54] 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])
total number of confs: 804
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277639 none CC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 54, 54, 54, 54, 54, 1, 1, 27, 27, 27, 27, 27, 27, 27, 22, 22, 6, 1, 1, 1, 1, 1, 1, 9, 9, 54, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277639 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277639
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277639/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277639
Building REAL300025277640
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277640'
/scratch/stefan/7808390/working/building/REAL300025277640 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277640

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277640/0 /scratch/stefan/7808390/working/building/REAL300025277640 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/520
`/scratch/stefan/7808390/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCC3)C2C1)

`REAL300025277640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277640 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 13, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 1, 1, 8, 8, 46, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 48, 49, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277640 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 12, 1, 1, 1, 1, 1, 1, 1, 33, 46, 46, 46, 46, 46, 109, 109, 109, 201, 201, 201, 201, 201, 46, 46, 28, 28, 1, 46, 46, 46, 46, 46, 46, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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, 44, 45, 46, 47, 48, 49])
total number of confs: 612
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277640 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 73, 115, 201, 201, 201, 201, 201, 27, 27, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 73, 73, 201, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 35, 47, 48, 49])
total number of confs: 508
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277640 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277640
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277640/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277640
Building REAL300025277641
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277641'
/scratch/stefan/7808390/working/building/REAL300025277641 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277641

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277641/0 /scratch/stefan/7808390/working/building/REAL300025277641 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/521
`/scratch/stefan/7808390/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC=N3)C2C1)

`REAL300025277641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277641 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 17, 35, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 17, 17, 120, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38])
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: REAL300025277641 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 51, 13, 1, 1, 1, 1, 1, 1, 1, 80, 120, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 51, 51, 1, 120, 120, 120, 120, 120, 120, 201, 201, 201, 201, 120, 120, 120] 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: 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: REAL300025277641 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 10, 20, 68, 117, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 68, 68, 201, 10, 10, 10, 10, 10, 10, 3, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [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, 34, 35, 39, 40, 41])
total number of confs: 476
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277641 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277641
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277641/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277641
Building REAL300025277642
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277642'
/scratch/stefan/7808390/working/building/REAL300025277642 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277642

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277642/0 /scratch/stefan/7808390/working/building/REAL300025277642 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/522
`/scratch/stefan/7808390/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277642 none CC1=CC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 37, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 18, 53, 53, 53, 53, 53, 1, 1, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 1, 1, 14, 14, 53, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277642 none CC1=CC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 9, 9, 9, 37, 37, 37, 37, 37, 59, 59, 113, 147, 201, 201, 201, 201, 201, 37, 37, 2, 2, 2, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 37, 113, 113, 201, 37, 37, 37] 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])
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: REAL300025277642 none CC1=CC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 107, 107, 107, 53, 53, 53, 53, 53, 36, 33, 36, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 201, 201, 107, 53, 53, 53, 53, 53, 53, 33, 33, 1, 53, 53, 53] 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])
total number of confs: 492
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277642 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277642
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277642/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277642
Building REAL300025277643
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277643'
/scratch/stefan/7808390/working/building/REAL300025277643 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277643

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277643/0 /scratch/stefan/7808390/working/building/REAL300025277643 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/523
`/scratch/stefan/7808390/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277643 none O=C(CC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 42, 42, 42, 42, 42, 1, 1, 36, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 6, 1, 1, 1, 1, 1, 1, 5, 5, 42, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277643 none O=C(CC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 20, 20, 55, 55, 55, 55, 55, 65, 65, 84, 125, 201, 201, 201, 201, 201, 55, 55, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 55, 55, 55, 55, 55, 55, 84, 84, 201, 55, 55, 55] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025277643 none O=C(CC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 198, 201, 201, 201, 201, 42, 42, 42, 42, 42, 30, 25, 30, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 42, 42, 42, 42, 42, 42, 25, 25, 1, 42, 42, 42] 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])
total number of confs: 805
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277643 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277643
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277643/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277643
Building REAL300025277644
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277644'
/scratch/stefan/7808390/working/building/REAL300025277644 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277644

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277644/0 /scratch/stefan/7808390/working/building/REAL300025277644 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/524
`/scratch/stefan/7808390/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277644 none O=C(CCC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 37, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 28, 28, 28, 28, 28, 1, 1, 33, 33, 38, 38, 57, 57, 57, 57, 57, 57, 57, 57, 57, 5, 1, 1, 1, 1, 1, 1, 4, 4, 28, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277644 none O=C(CCC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 20, 20, 57, 57, 57, 57, 57, 65, 65, 87, 126, 201, 201, 201, 201, 201, 57, 57, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 57, 57, 57, 57, 57, 57, 87, 87, 201, 57, 57, 57] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 39, 35, 36, 38, 37, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277644 none O=C(CCC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 149, 154, 201, 201, 201, 201, 28, 28, 28, 28, 28, 23, 21, 23, 11, 1, 1, 1, 1, 1, 1, 1, 28, 28, 149, 149, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 28, 28, 28, 28, 28, 28, 21, 21, 1, 28, 28, 28] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 796
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277644 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277644
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277644/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277644
Building REAL300025277645
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277645'
/scratch/stefan/7808390/working/building/REAL300025277645 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277645

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277645/0 /scratch/stefan/7808390/working/building/REAL300025277645 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/525
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=CC(F)=C3)C2C1)

`REAL300025277645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277645 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 9, 9, 46, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40])
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: REAL300025277645 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 12, 1, 1, 1, 1, 1, 1, 1, 32, 46, 46, 46, 46, 46, 69, 69, 69, 201, 201, 201, 201, 201, 201, 46, 46, 27, 27, 1, 46, 46, 46, 46, 46, 46, 69, 201, 201, 201, 201, 46, 46, 46] 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: 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: REAL300025277645 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 20, 35, 70, 113, 201, 201, 201, 201, 201, 20, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 20, 20, 70, 70, 201, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 505
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277645 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277645
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277645/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277645
Building REAL300025277646
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277646'
/scratch/stefan/7808390/working/building/REAL300025277646 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277646

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277646/0 /scratch/stefan/7808390/working/building/REAL300025277646 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/526
`/scratch/stefan/7808390/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CS3)C2C1)

`REAL300025277646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277646 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 19, 37, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 1, 1, 19, 19, 131, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
total number of confs: 239
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277646 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 46, 13, 1, 1, 1, 1, 1, 1, 1, 88, 131, 131, 131, 131, 131, 177, 177, 177, 201, 201, 201, 201, 131, 131, 46, 46, 1, 131, 131, 131, 131, 131, 131, 177, 201, 201, 201, 131, 131, 131] 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: 569
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277646 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 15, 27, 63, 107, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 15, 15, 63, 63, 201, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 15, 15, 15] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 470
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277646 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277646
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277646/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277646
Building REAL300025277647
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277647'
/scratch/stefan/7808390/working/building/REAL300025277647 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277647

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277647/0 /scratch/stefan/7808390/working/building/REAL300025277647 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/527
`/scratch/stefan/7808390/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1)

`REAL300025277647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277647 none CC1=CN=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 48, 127, 127, 127, 127, 127, 1, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 28, 28, 127, 1, 1, 1, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277647 none CC1=CN=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 32, 32, 103, 142, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 4, 11, 11, 11, 11, 11, 11, 103, 103, 201, 11, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 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])
total number of confs: 555
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277647 none CC1=CN=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 81, 42, 81, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 127, 42, 42, 1, 127, 127, 127, 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])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277647 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277647
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277647/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277647
Building REAL300025277648
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277648'
/scratch/stefan/7808390/working/building/REAL300025277648 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277648

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277648/0 /scratch/stefan/7808390/working/building/REAL300025277648 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/528
`/scratch/stefan/7808390/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CSC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277648 none O=C(CC1=CSC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 14, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 21, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 37, 37, 37, 37, 37, 1, 1, 21, 21, 40, 40, 40, 6, 1, 1, 1, 1, 1, 1, 8, 8, 37, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277648 none O=C(CC1=CSC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 14, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 40, 40, 40, 40, 65, 65, 97, 150, 201, 201, 201, 201, 201, 40, 40, 3, 3, 1, 1, 1, 9, 40, 40, 40, 40, 40, 40, 97, 97, 201, 40, 40, 40] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025277648 none O=C(CC1=CSC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 14, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 116, 201, 201, 201, 201, 37, 37, 37, 37, 37, 27, 27, 27, 12, 1, 1, 1, 1, 1, 1, 1, 37, 37, 116, 116, 201, 201, 201, 65, 37, 37, 37, 37, 37, 37, 27, 27, 1, 37, 37, 37] 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])
total number of confs: 605
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277648 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277648
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277648/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277648
Building REAL300025277649
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277649'
/scratch/stefan/7808390/working/building/REAL300025277649 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277649

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277649/0 /scratch/stefan/7808390/working/building/REAL300025277649 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/529
`/scratch/stefan/7808390/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277649 none CC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 13, 64, 64, 64, 64, 64, 1, 1, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 8, 8, 64, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277649 none CC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 11, 11, 11, 31, 31, 31, 31, 31, 44, 44, 76, 113, 201, 201, 201, 201, 201, 31, 31, 2, 2, 2, 1, 1, 1, 1, 11, 31, 31, 31, 31, 31, 31, 76, 76, 201, 31, 31, 31] 201
rigid atoms, others: [0, 1, 2, 3, 4, 27, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 524
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277649 none CC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 112, 112, 112, 64, 64, 64, 64, 64, 47, 41, 47, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 112, 64, 64, 64, 64, 64, 64, 41, 41, 1, 64, 64, 64] 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])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277649 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277649
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277649/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277649
Building REAL300025277650
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277650'
/scratch/stefan/7808390/working/building/REAL300025277650 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277650

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277650/0 /scratch/stefan/7808390/working/building/REAL300025277650 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/530
`/scratch/stefan/7808390/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277650 none CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 22, 77, 77, 77, 77, 77, 1, 1, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 13, 13, 77, 1, 1, 1, 13] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
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: REAL300025277650 none CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 13, 13, 13, 13, 13, 28, 28, 65, 108, 201, 201, 201, 201, 201, 13, 13, 1, 2, 2, 2, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 65, 65, 201, 13, 13, 13, 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: 507
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: REAL300025277650 none CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 96, 96, 96, 77, 77, 77, 77, 77, 63, 49, 63, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 201, 201, 96, 77, 77, 77, 77, 77, 77, 49, 49, 1, 77, 77, 77, 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])
total number of confs: 464
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277650 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277650
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277650/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277650
Building REAL300025277651
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277651'
/scratch/stefan/7808390/working/building/REAL300025277651 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277651

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277651/0 /scratch/stefan/7808390/working/building/REAL300025277651 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/531
`/scratch/stefan/7808390/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277651 none CCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 112, 112, 112, 51, 51, 51, 51, 51, 33, 26, 33, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 112, 51, 51, 51, 51, 51, 51, 26, 26, 1, 51, 51, 51] 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])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277651 none CCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 51, 51, 51, 51, 51, 1, 1, 30, 30, 30, 30, 30, 23, 23, 6, 1, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277651 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277651
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277651/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277651
Building REAL300025277652
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277652'
/scratch/stefan/7808390/working/building/REAL300025277652 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277652

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277652/0 /scratch/stefan/7808390/working/building/REAL300025277652 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/532
`/scratch/stefan/7808390/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277652 none CC(C)=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 132, 132, 132, 67, 67, 67, 67, 67, 46, 40, 46, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 132, 67, 67, 67, 67, 67, 67, 40, 40, 1, 67, 67, 67] 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])
total number of confs: 668
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277652 none CC(C)=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 67, 67, 67, 67, 67, 1, 1, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 9, 9, 67, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277652 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277652
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277652/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277652
Building REAL300025277653
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277653'
/scratch/stefan/7808390/working/building/REAL300025277653 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277653

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277653/0 /scratch/stefan/7808390/working/building/REAL300025277653 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/533
`/scratch/stefan/7808390/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCO3)C2C1)

`REAL300025277653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277653 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 16, 31, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 16, 16, 118, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 212
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277653 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 49, 13, 1, 1, 1, 1, 1, 1, 1, 78, 118, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 49, 49, 1, 118, 118, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 118, 118, 118] 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: 621
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277653 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 12, 23, 70, 114, 201, 201, 201, 201, 201, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 70, 70, 201, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 12, 12, 12] 201
rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42, 43])
total number of confs: 489
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277653 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277653
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277653/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277653
Building REAL300025277654
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277654'
/scratch/stefan/7808390/working/building/REAL300025277654 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277654

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277654/0 /scratch/stefan/7808390/working/building/REAL300025277654 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/534
`/scratch/stefan/7808390/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=[N+]([O-])C=C3)C2C1)

`REAL300025277654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277654 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=[N+]([O-])C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [6, 1, 6, 15, 31, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 15, 15, 104, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277654 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=[N+]([O-])C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [66, 44, 13, 1, 1, 1, 1, 1, 1, 1, 66, 104, 104, 104, 104, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 44, 44, 1, 104, 104, 104, 104, 104, 104, 201, 201, 201, 201, 201, 104, 104, 104] 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: 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: REAL300025277654 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=[N+]([O-])C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [30, 11, 30, 73, 124, 201, 201, 201, 201, 201, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 73, 73, 201, 11, 11, 11, 11, 11, 11, 3, 1, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 494
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277654 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277654
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277654/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277654
Building REAL300025277655
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277655'
/scratch/stefan/7808390/working/building/REAL300025277655 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277655

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277655/0 /scratch/stefan/7808390/working/building/REAL300025277655 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/535
`/scratch/stefan/7808390/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3C4)C2C1)

`REAL300025277655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277655 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 23, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 1, 1, 13, 13, 90, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 46, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 179
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277655 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 65, 90, 90, 90, 90, 90, 157, 157, 157, 201, 201, 201, 201, 201, 201, 90, 90, 42, 42, 1, 90, 90, 90, 90, 90, 90, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90] 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])
total number of confs: 660
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277655 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 29, 68, 98, 201, 201, 201, 201, 201, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 17, 17, 68, 68, 201, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48])
total number of confs: 481
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277655 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277655
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277655/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277655
Building REAL300025277656
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277656'
/scratch/stefan/7808390/working/building/REAL300025277656 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277656

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277656/0 /scratch/stefan/7808390/working/building/REAL300025277656 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/536
`/scratch/stefan/7808390/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277656 none CC(=O)NC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 139, 201, 139, 139, 59, 59, 59, 59, 59, 36, 28, 36, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 139, 59, 59, 59, 59, 59, 59, 28, 28, 1, 59, 59, 59] 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])
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: REAL300025277656 none CC(=O)NC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 6, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 59, 59, 59, 59, 59, 1, 1, 30, 30, 30, 30, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 5, 5, 59, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277656 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277656
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277656/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277656
Building REAL300025277657
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277657'
/scratch/stefan/7808390/working/building/REAL300025277657 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277657

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277657/0 /scratch/stefan/7808390/working/building/REAL300025277657 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/537
`/scratch/stefan/7808390/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNC(=O)C=C3)C2C1)

`REAL300025277657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277657 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNC(=O)C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [3, 1, 3, 11, 27, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 1, 1, 11, 11, 119, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 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: REAL300025277657 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNC(=O)C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [80, 50, 13, 1, 1, 1, 1, 1, 1, 1, 80, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 50, 50, 1, 119, 119, 119, 119, 119, 119, 201, 201, 201, 201, 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, 42])
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: REAL300025277657 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNC(=O)C=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [35, 23, 35, 75, 118, 201, 201, 201, 201, 201, 23, 23, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 75, 75, 201, 23, 23, 23, 23, 23, 23, 7, 1, 1, 1, 23, 23, 23] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 499
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277657 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277657
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277657/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277657
Building REAL300025277658
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277658'
/scratch/stefan/7808390/working/building/REAL300025277658 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277658

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277658/0 /scratch/stefan/7808390/working/building/REAL300025277658 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/538
`/scratch/stefan/7808390/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277658 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 124, 124, 124, 124, 124, 1, 1, 15, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 26, 26, 124, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 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: REAL300025277658 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 5, 5, 5, 16, 16, 16, 16, 16, 34, 34, 103, 143, 201, 201, 201, 201, 201, 16, 16, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 16, 16, 103, 103, 201, 16, 16, 16] 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])
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: REAL300025277658 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 200, 200, 200, 124, 124, 124, 124, 124, 79, 43, 79, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 200, 124, 124, 124, 124, 124, 124, 43, 43, 1, 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])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277658 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277658
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277658/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277658
Building REAL300025277659
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277659'
/scratch/stefan/7808390/working/building/REAL300025277659 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277659

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277659/0 /scratch/stefan/7808390/working/building/REAL300025277659 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/539
`/scratch/stefan/7808390/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277659 none O=C(CC1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 35, 35, 35, 35, 35, 1, 1, 32, 32, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 1, 1, 1, 1, 1, 1, 4, 4, 35, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277659 none O=C(CC1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 46, 46, 46, 46, 46, 54, 54, 76, 115, 201, 201, 201, 201, 201, 46, 46, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 46, 46, 46, 46, 46, 46, 76, 76, 201, 46, 46, 46] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 37, 35, 36, 38, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277659 none O=C(CC1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 200, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 25, 22, 25, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 35, 35, 35, 35, 35, 35, 22, 22, 1, 35, 35, 35] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 742
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277659 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277659
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277659/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277659
Building REAL300025277660
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277660'
/scratch/stefan/7808390/working/building/REAL300025277660 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277660

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277660/0 /scratch/stefan/7808390/working/building/REAL300025277660 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/540
`/scratch/stefan/7808390/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCO3)C2C1)

`REAL300025277660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277660 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens need 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, 10, 22, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 1, 1, 10, 10, 91, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 23, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277660 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 62, 91, 91, 91, 91, 91, 176, 176, 176, 201, 201, 201, 201, 91, 91, 43, 43, 1, 91, 91, 91, 91, 91, 91, 176, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91] 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: 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: REAL300025277660 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens 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, 20, 33, 72, 113, 201, 201, 201, 201, 201, 20, 20, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 20, 20, 72, 72, 201, 20, 20, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44])
total number of confs: 507
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277660 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277660
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277660/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277660
Building REAL300025277661
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277661'
/scratch/stefan/7808390/working/building/REAL300025277661 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277661

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277661/0 /scratch/stefan/7808390/working/building/REAL300025277661 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/541
`/scratch/stefan/7808390/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277661 none CSCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 111, 111, 111, 41, 41, 41, 41, 41, 27, 21, 27, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 111, 41, 41, 41, 41, 41, 41, 21, 21, 1, 41, 41, 41] 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])
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: REAL300025277661 none CSCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [30, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 41, 41, 41, 41, 41, 1, 1, 30, 30, 30, 26, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 41, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 39, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 35, 36, 37])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277661 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277661
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277661/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277661
Building REAL300025277662
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277662'
/scratch/stefan/7808390/working/building/REAL300025277662 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277662

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277662/0 /scratch/stefan/7808390/working/building/REAL300025277662 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/542
`/scratch/stefan/7808390/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1)

`REAL300025277662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277662 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 48, 125, 125, 125, 125, 125, 1, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 27, 27, 125, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
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: REAL300025277662 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 3, 3, 11, 11, 11, 11, 11, 32, 32, 101, 147, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 11, 11, 101, 101, 201, 11, 11, 11] 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: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277662 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 125, 125, 125, 125, 125, 77, 41, 77, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 125, 41, 41, 1, 125, 125, 125] 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])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277662 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277662
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277662/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277662
Building REAL300025277663
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277663'
/scratch/stefan/7808390/working/building/REAL300025277663 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277663

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277663/0 /scratch/stefan/7808390/working/building/REAL300025277663 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/543
`/scratch/stefan/7808390/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277663 none CSCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 175, 175, 144, 144, 144, 59, 59, 59, 59, 59, 38, 31, 38, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 175, 175, 175, 175, 144, 59, 59, 59, 59, 59, 59, 31, 31, 1, 59, 59, 59] 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])
total number of confs: 662
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277663 none CSCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [41, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 59, 59, 59, 59, 59, 1, 1, 41, 41, 41, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 5, 5, 59, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277663 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277663
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277663/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277663
Building REAL300025277664
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277664'
/scratch/stefan/7808390/working/building/REAL300025277664 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277664

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277664/0 /scratch/stefan/7808390/working/building/REAL300025277664 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/544
`/scratch/stefan/7808390/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277664 none CC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 88, 88, 88, 36, 36, 36, 36, 36, 27, 22, 27, 11, 1, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 88, 36, 36, 36, 36, 36, 36, 22, 22, 1, 36, 36, 36] 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])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277664 none CC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 36, 36, 36, 36, 36, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 5, 36, 1, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277664 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277664
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277664/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277664
Building REAL300025277665
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277665'
/scratch/stefan/7808390/working/building/REAL300025277665 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277665

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277665/0 /scratch/stefan/7808390/working/building/REAL300025277665 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/545
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CSC=C3)C2C1)

`REAL300025277665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277665 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 21, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 1, 1, 12, 12, 63, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
total number of confs: 136
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277665 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 31, 13, 1, 1, 1, 1, 1, 1, 1, 41, 63, 63, 63, 63, 63, 122, 122, 122, 201, 201, 201, 201, 63, 63, 31, 31, 1, 63, 63, 63, 63, 63, 63, 122, 201, 201, 201, 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])
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: REAL300025277665 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 18, 37, 76, 118, 201, 201, 201, 201, 201, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 18, 18, 76, 76, 201, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 18, 18, 18] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 523
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277665 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277665
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277665/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277665
Building REAL300025277666
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277666'
/scratch/stefan/7808390/working/building/REAL300025277666 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277666

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277666/0 /scratch/stefan/7808390/working/building/REAL300025277666 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/546
`/scratch/stefan/7808390/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1)

`REAL300025277666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277666 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 84, 84, 84, 84, 84, 1, 1, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 10, 10, 84, 1, 1, 1, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43])
total number of confs: 158
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: REAL300025277666 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 19, 19, 19, 19, 19, 31, 31, 68, 104, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 2, 2, 2, 7, 19, 19, 19, 19, 19, 19, 68, 68, 201, 19, 19, 19, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 43, 23, 24, 25] set([4, 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])
total number of confs: 512
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: REAL300025277666 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
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, 84, 84, 84, 84, 84, 58, 41, 58, 12, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 133, 84, 84, 84, 84, 84, 84, 41, 41, 1, 84, 84, 84, 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])
total number of confs: 539
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277666 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277666
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277666/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277666
Building REAL300025277667
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277667'
/scratch/stefan/7808390/working/building/REAL300025277667 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277667

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277667/0 /scratch/stefan/7808390/working/building/REAL300025277667 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/547
`/scratch/stefan/7808390/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1C=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277667 none O=C(CC1C=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 1, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 8, 44, 44, 44, 44, 44, 1, 1, 38, 38, 52, 52, 52, 52, 52, 52, 52, 6, 1, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 244
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277667 none O=C(CC1C=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 1, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 52, 52, 52, 52, 52, 62, 62, 85, 131, 201, 201, 201, 201, 201, 52, 52, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 52, 52, 52, 52, 52, 52, 85, 85, 201, 52, 52, 52] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277667 none O=C(CC1C=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 1, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 196, 201, 201, 201, 201, 44, 44, 44, 44, 44, 33, 27, 33, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 196, 196, 201, 201, 201, 201, 201, 201, 201, 96, 44, 44, 44, 44, 44, 44, 27, 27, 1, 44, 44, 44] 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])
total number of confs: 758
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277667 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277667
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277667/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277667
Building REAL300025277668
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277668'
/scratch/stefan/7808390/working/building/REAL300025277668 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277668

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277668/0 /scratch/stefan/7808390/working/building/REAL300025277668 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/548
`/scratch/stefan/7808390/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277668 none O=C(CN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 1, 8, 8, 8, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 28, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 60, 60, 60, 60, 60, 1, 1, 28, 28, 43, 6, 1, 1, 1, 1, 1, 1, 6, 6, 60, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 36, 37, 38])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277668 none O=C(CN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 1, 8, 8, 8, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 16, 16, 43, 43, 43, 43, 43, 57, 57, 86, 123, 201, 201, 201, 201, 201, 43, 43, 5, 5, 1, 16, 43, 43, 43, 43, 43, 43, 86, 86, 201, 43, 43, 43] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28] set([0, 1, 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: 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: REAL300025277668 none O=C(CN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 1, 8, 8, 8, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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: [142, 142, 142, 201, 201, 201, 201, 201, 60, 60, 60, 60, 60, 36, 32, 36, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 142, 60, 60, 60, 60, 60, 60, 32, 32, 1, 60, 60, 60] 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])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277668 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277668
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277668/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277668
Building REAL300025277669
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277669'
/scratch/stefan/7808390/working/building/REAL300025277669 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277669

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277669/0 /scratch/stefan/7808390/working/building/REAL300025277669 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/549
`/scratch/stefan/7808390/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCCC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277669 none O=C(CN1CCCC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 56, 56, 56, 56, 56, 1, 1, 29, 29, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 1, 1, 5, 5, 56, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277669 none O=C(CN1CCCC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 36, 36, 36, 49, 49, 71, 115, 201, 201, 201, 201, 201, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 14, 36, 36, 36, 36, 36, 36, 71, 71, 201, 36, 36, 36] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: REAL300025277669 none O=C(CN1CCCC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 201, 201, 201, 201, 201, 201, 56, 56, 56, 56, 56, 36, 29, 36, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 132, 56, 56, 56, 56, 56, 56, 29, 29, 1, 56, 56, 56] 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])
total number of confs: 743
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277669 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277669
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277669/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277669
Building REAL300025277670
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277670'
/scratch/stefan/7808390/working/building/REAL300025277670 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277670

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277670/0 /scratch/stefan/7808390/working/building/REAL300025277670 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/550
`/scratch/stefan/7808390/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1)

`REAL300025277670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277670 none CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 27, 82, 82, 82, 82, 82, 1, 1, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 13, 13, 82, 1, 1, 1, 10] 105
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 158
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277670 none CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 19, 19, 43, 63, 105, 105, 105, 105, 105, 10, 10, 1, 1, 2, 2, 2, 1, 5, 10, 10, 10, 10, 10, 10, 43, 43, 105, 10, 10, 10, 1] 105
rigid atoms, others: [0, 1, 2, 3, 4, 43, 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: 282
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: REAL300025277670 none CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 100, 100, 100, 82, 82, 82, 82, 82, 66, 47, 66, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 105, 105, 105, 105, 105, 105, 100, 82, 82, 82, 82, 82, 82, 47, 47, 1, 82, 82, 82, 105] 105
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: 330
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277670 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277670
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277670/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277670
Building REAL300025277671
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277671'
/scratch/stefan/7808390/working/building/REAL300025277671 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277671

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277671/0 /scratch/stefan/7808390/working/building/REAL300025277671 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/551
`/scratch/stefan/7808390/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277671 none CC1=NOC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 75, 75, 75, 75, 75, 1, 1, 20, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 10, 10, 75, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 143
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: REAL300025277671 none CC1=NOC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 10, 10, 10, 20, 20, 20, 20, 20, 32, 32, 68, 101, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 2, 2, 2, 10, 20, 20, 20, 20, 20, 20, 68, 68, 201, 20, 20, 20] 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])
total number of confs: 518
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: REAL300025277671 none CC1=NOC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 120, 120, 120, 75, 75, 75, 75, 75, 54, 37, 54, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 201, 120, 75, 75, 75, 75, 75, 75, 37, 37, 1, 75, 75, 75] 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])
total number of confs: 516
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277671 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277671
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277671/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277671
Building REAL300025277672
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277672'
/scratch/stefan/7808390/working/building/REAL300025277672 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277672

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277672/0 /scratch/stefan/7808390/working/building/REAL300025277672 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/552
`/scratch/stefan/7808390/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SN=N1)

`REAL300025277672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277672 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 18, 77, 77, 77, 77, 77, 1, 1, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 9, 9, 77, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38])
total number of confs: 151
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: REAL300025277672 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 8, 8, 8, 22, 22, 22, 22, 22, 32, 32, 72, 113, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 72, 72, 201, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 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])
total number of confs: 521
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: REAL300025277672 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 135, 135, 135, 77, 77, 77, 77, 77, 58, 44, 58, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 201, 135, 77, 77, 77, 77, 77, 77, 44, 44, 1, 77, 77, 77] 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])
total number of confs: 559
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277672 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277672
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277672/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277672
Building REAL300025277673
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277673'
/scratch/stefan/7808390/working/building/REAL300025277673 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277673

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277673/0 /scratch/stefan/7808390/working/building/REAL300025277673 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/553
`/scratch/stefan/7808390/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1)

`REAL300025277673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277673 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 15, 29, 29, 29, 29, 29, 1, 1, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 10, 10, 29, 1, 1, 1, 10, 10, 10] 39
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46])
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: REAL300025277673 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
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, 6, 6, 6, 10, 10, 10, 10, 10, 19, 19, 23, 30, 39, 39, 39, 39, 39, 10, 10, 1, 1, 1, 2, 2, 2, 1, 6, 10, 10, 10, 10, 10, 10, 23, 23, 39, 10, 10, 10, 2, 2, 2] 39
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 30] set([5, 6, 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, 45, 46])
total number of confs: 116
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277673 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
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, 38, 38, 38, 29, 29, 29, 29, 29, 24, 21, 24, 10, 1, 1, 1, 1, 1, 1, 1, 29, 29, 39, 39, 39, 39, 39, 39, 39, 38, 29, 29, 29, 29, 29, 29, 21, 21, 1, 29, 29, 29, 39, 39, 39] 39
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: 116
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277673 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277673
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277673/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277673
Building REAL300025277674
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277674'
/scratch/stefan/7808390/working/building/REAL300025277674 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277674

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277674/0 /scratch/stefan/7808390/working/building/REAL300025277674 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/554
`/scratch/stefan/7808390/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CCC3)C2C1)

`REAL300025277674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277674 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 16, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 26, 26, 1, 1, 9, 9, 70, 1, 1, 1, 1, 1, 1, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 169
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: REAL300025277674 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 55, 70, 70, 70, 70, 70, 119, 119, 119, 201, 201, 201, 201, 201, 70, 70, 35, 35, 1, 70, 70, 70, 70, 70, 70, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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])
total number of confs: 660
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: REAL300025277674 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 37, 75, 114, 201, 201, 201, 201, 201, 26, 26, 26, 26, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 75, 75, 201, 26, 26, 26, 26, 26, 26, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 35, 45, 46, 47])
total number of confs: 520
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277674 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277674
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277674/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277674
Building REAL300025277675
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277675'
/scratch/stefan/7808390/working/building/REAL300025277675 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277675

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277675/0 /scratch/stefan/7808390/working/building/REAL300025277675 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/555
`/scratch/stefan/7808390/working/3D/555' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277675 none CC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 125, 125, 125, 125, 125, 1, 1, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 26, 26, 125, 1, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 36, 37, 38, 42])
total number of confs: 260
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277675 none CC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 4, 14, 14, 14, 14, 14, 36, 36, 105, 148, 201, 201, 201, 201, 201, 14, 14, 1, 2, 2, 2, 4, 14, 14, 14, 14, 14, 14, 105, 105, 201, 14, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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])
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: REAL300025277675 none CC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 200, 200, 125, 125, 125, 125, 125, 75, 42, 75, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 200, 125, 125, 125, 125, 125, 125, 42, 42, 1, 125, 125, 125, 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])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277675 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277675
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277675/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277675
Building REAL300025277676
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277676'
/scratch/stefan/7808390/working/building/REAL300025277676 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277676

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277676/0 /scratch/stefan/7808390/working/building/REAL300025277676 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/556
`/scratch/stefan/7808390/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN3)C2C1)

`REAL300025277676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277676 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 15, 31, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 1, 1, 15, 15, 112, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 41, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38])
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: REAL300025277676 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 46, 13, 1, 1, 1, 1, 1, 1, 1, 76, 112, 112, 112, 112, 112, 176, 176, 176, 201, 201, 201, 201, 112, 112, 46, 46, 1, 112, 112, 112, 112, 112, 112, 176, 201, 201, 201, 201, 112, 112, 112] 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: 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: REAL300025277676 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 17, 27, 65, 116, 201, 201, 201, 201, 201, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 17, 17, 65, 65, 201, 17, 17, 17, 17, 17, 17, 4, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [35, 36, 37, 38, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 470
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277676 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277676
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277676/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277676
Building REAL300025277677
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277677'
/scratch/stefan/7808390/working/building/REAL300025277677 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277677

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277677/0 /scratch/stefan/7808390/working/building/REAL300025277677 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/557
`/scratch/stefan/7808390/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(Cl)=CN3)C2C1)

`REAL300025277677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277677 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(Cl)=CN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 13, 28, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 1, 13, 13, 103, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277677 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(Cl)=CN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 45, 13, 1, 1, 1, 1, 1, 1, 1, 67, 103, 103, 103, 103, 103, 184, 184, 184, 201, 201, 201, 201, 201, 103, 103, 45, 45, 1, 103, 103, 103, 103, 103, 103, 184, 201, 201, 201, 103, 103, 103] 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: 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: REAL300025277677 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(Cl)=CN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 17, 28, 67, 112, 201, 201, 201, 201, 201, 17, 17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 67, 67, 201, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [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, 34, 35, 39, 40, 41])
total number of confs: 485
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277677 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277677
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277677/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277677
Building REAL300025277678
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277678'
/scratch/stefan/7808390/working/building/REAL300025277678 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277678

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277678/0 /scratch/stefan/7808390/working/building/REAL300025277678 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/558
`/scratch/stefan/7808390/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277678 none CC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 201, 201, 173, 176, 85, 85, 85, 35, 35, 35, 35, 35, 23, 19, 23, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 190, 188, 197, 197, 176, 176, 85, 35, 35, 35, 35, 35, 35, 19, 19, 1, 35, 35, 35] 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])
total number of confs: 941
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277678 none CC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 23, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 35, 35, 35, 35, 35, 1, 1, 36, 36, 36, 31, 30, 31, 31, 24, 24, 5, 1, 1, 1, 1, 1, 1, 5, 5, 35, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 260
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277678 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277678
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277678/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277678
Building REAL300025277679
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277679'
/scratch/stefan/7808390/working/building/REAL300025277679 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277679

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277679/0 /scratch/stefan/7808390/working/building/REAL300025277679 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/559
`/scratch/stefan/7808390/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1C)

`REAL300025277679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277679 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 80, 80, 80, 80, 80, 1, 1, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 16, 16, 80, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47])
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: REAL300025277679 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 20, 20, 20, 20, 20, 41, 41, 105, 141, 201, 201, 201, 201, 201, 20, 20, 1, 1, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 20, 20, 105, 105, 201, 20, 20, 20, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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, 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: REAL300025277679 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1C 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 139, 139, 139, 80, 80, 80, 80, 80, 50, 36, 50, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 139, 80, 80, 80, 80, 80, 80, 36, 36, 1, 80, 80, 80, 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])
total number of confs: 548
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277679 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277679
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277679/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277679
Building REAL300025277680
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277680'
/scratch/stefan/7808390/working/building/REAL300025277680 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277680

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277680/0 /scratch/stefan/7808390/working/building/REAL300025277680 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/560
`/scratch/stefan/7808390/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=C3)C2C1)

`REAL300025277680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277680 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 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: [3, 1, 3, 13, 25, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 1, 1, 13, 13, 89, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
total number of confs: 170
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: REAL300025277680 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 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: [62, 44, 13, 1, 1, 1, 1, 1, 1, 1, 62, 89, 89, 89, 89, 89, 144, 144, 144, 201, 201, 201, 201, 89, 89, 44, 44, 1, 89, 89, 89, 89, 89, 89, 144, 201, 201, 201, 89, 89, 89] 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: 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: REAL300025277680 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 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: [29, 16, 29, 68, 113, 201, 201, 201, 201, 201, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 16, 16, 68, 68, 201, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 16, 16, 16] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 514
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277680 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277680
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277680/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277680
Building REAL300025277681
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277681'
/scratch/stefan/7808390/working/building/REAL300025277681 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277681

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277681/0 /scratch/stefan/7808390/working/building/REAL300025277681 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/561
`/scratch/stefan/7808390/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277681 none O=C(CN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 26, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 61, 61, 61, 61, 61, 1, 1, 26, 26, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 5, 61, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277681 none O=C(CN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 1, 1, 12, 12, 34, 34, 34, 34, 34, 46, 46, 69, 111, 201, 201, 201, 201, 201, 34, 34, 7, 7, 1, 1, 1, 12, 34, 34, 34, 34, 34, 34, 69, 69, 201, 34, 34, 34] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277681 none O=C(CN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [149, 149, 149, 201, 201, 201, 201, 201, 61, 61, 61, 61, 61, 37, 30, 37, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 149, 61, 61, 61, 61, 61, 61, 30, 30, 1, 61, 61, 61] 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])
total number of confs: 748
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277681 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277681
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277681/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277681
Building REAL300025277682
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277682'
/scratch/stefan/7808390/working/building/REAL300025277682 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277682

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277682/0 /scratch/stefan/7808390/working/building/REAL300025277682 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/562
`/scratch/stefan/7808390/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=C1)

`REAL300025277682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277682 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 19, 79, 79, 79, 79, 79, 1, 1, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 9, 9, 79, 1, 1, 1, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277682 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 6, 6, 6, 19, 19, 19, 19, 19, 30, 30, 70, 116, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 2, 2, 2, 6, 19, 19, 19, 19, 19, 19, 70, 70, 201, 19, 19, 19, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 43, 23, 24, 25] set([4, 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])
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: REAL300025277682 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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.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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 174, 174, 174, 79, 79, 79, 79, 79, 53, 39, 53, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 201, 201, 174, 79, 79, 79, 79, 79, 79, 39, 39, 1, 79, 79, 79, 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])
total number of confs: 579
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277682 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277682
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277682/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277682
Building REAL300025277683
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277683'
/scratch/stefan/7808390/working/building/REAL300025277683 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277683

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277683/0 /scratch/stefan/7808390/working/building/REAL300025277683 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/563
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CC4CCC3C4)C2C1)

`REAL300025277683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277683 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4CCC3C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 19, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 1, 1, 10, 10, 70, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277683 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4CCC3C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 51, 70, 70, 70, 70, 70, 144, 144, 144, 201, 201, 201, 201, 201, 201, 70, 70, 38, 38, 1, 70, 70, 70, 70, 70, 70, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70] 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: 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: REAL300025277683 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4CCC3C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 23, 34, 72, 110, 201, 201, 201, 201, 201, 23, 23, 23, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 72, 72, 201, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 500
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277683 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277683
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277683/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277683
Building REAL300025277684
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277684'
/scratch/stefan/7808390/working/building/REAL300025277684 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277684

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277684/0 /scratch/stefan/7808390/working/building/REAL300025277684 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/564
`/scratch/stefan/7808390/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(Cl)O3)C2C1)

`REAL300025277684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277684 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(Cl)O3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 16, 31, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 16, 16, 108, 1, 1, 1, 1, 1, 1, 6, 13, 13, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 40, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277684 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(Cl)O3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 13, 1, 1, 1, 1, 1, 1, 1, 75, 108, 108, 108, 108, 108, 198, 198, 198, 201, 201, 201, 201, 201, 108, 108, 49, 49, 1, 108, 108, 108, 108, 108, 108, 198, 201, 201, 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, 40])
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: REAL300025277684 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(Cl)O3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 13, 23, 68, 116, 201, 201, 201, 201, 201, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 68, 68, 201, 13, 13, 13, 13, 13, 13, 4, 1, 1, 13, 13, 13] 201
rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 476
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277684 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277684
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277684/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277684
Building REAL300025277685
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277685'
/scratch/stefan/7808390/working/building/REAL300025277685 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277685

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277685/0 /scratch/stefan/7808390/working/building/REAL300025277685 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/565
`/scratch/stefan/7808390/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=NN1C)

`REAL300025277685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277685 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 18, 52, 52, 52, 52, 52, 1, 1, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 14, 14, 52, 1, 1, 1, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277685 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 27, 27, 27, 27, 27, 48, 48, 105, 142, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 1, 2, 2, 2, 8, 27, 27, 27, 27, 27, 27, 105, 105, 201, 27, 27, 27, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 43, 23, 24, 25, 26] set([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, 42, 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: REAL300025277685 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 107, 107, 107, 52, 52, 52, 52, 52, 35, 30, 35, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 107, 52, 52, 52, 52, 52, 52, 30, 30, 1, 52, 52, 52, 201, 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: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277685 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277685
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277685/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277685
Building REAL300025277686
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277686'
/scratch/stefan/7808390/working/building/REAL300025277686 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277686

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277686/0 /scratch/stefan/7808390/working/building/REAL300025277686 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/566
`/scratch/stefan/7808390/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277686 none CCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 64, 64, 64, 26, 26, 26, 26, 26, 21, 18, 21, 10, 1, 1, 1, 1, 1, 1, 1, 26, 26, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 64, 26, 26, 26, 26, 26, 26, 18, 18, 1, 26, 26, 26] 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])
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: REAL300025277686 none CCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 43, 36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 26, 26, 26, 26, 26, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 36, 36, 6, 1, 1, 1, 1, 1, 1, 4, 4, 26, 1, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277686 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277686
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277686/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277686
Building REAL300025277687
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277687'
/scratch/stefan/7808390/working/building/REAL300025277687 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277687

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277687/0 /scratch/stefan/7808390/working/building/REAL300025277687 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/567
`/scratch/stefan/7808390/working/3D/567' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277687 none CC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 131, 131, 131, 72, 72, 72, 72, 72, 49, 34, 49, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 72, 72, 72, 72, 72, 72, 34, 34, 1, 72, 72, 72] 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])
total number of confs: 815
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277687 none CC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 19, 72, 72, 72, 72, 72, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 6, 1, 1, 1, 1, 1, 1, 9, 9, 72, 1, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277687 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277687
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277687/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277687
Building REAL300025277688
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277688'
/scratch/stefan/7808390/working/building/REAL300025277688 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277688

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277688/0 /scratch/stefan/7808390/working/building/REAL300025277688 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/568
`/scratch/stefan/7808390/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1)

`REAL300025277688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277688 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 26, 82, 82, 82, 82, 82, 1, 1, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 13, 13, 82, 1, 1, 1, 10] 108
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
total number of confs: 156
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277688 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 18, 18, 41, 61, 108, 108, 108, 108, 108, 10, 10, 1, 1, 2, 2, 2, 1, 1, 5, 10, 10, 10, 10, 10, 10, 41, 41, 108, 10, 10, 10, 1] 108
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 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])
total number of confs: 282
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: REAL300025277688 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 100, 100, 100, 82, 82, 82, 82, 82, 66, 50, 66, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 108, 108, 108, 108, 108, 108, 108, 100, 82, 82, 82, 82, 82, 82, 50, 50, 1, 82, 82, 82, 108] 108
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: 331
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277688 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277688
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277688/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277688
Building REAL300025277689
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277689'
/scratch/stefan/7808390/working/building/REAL300025277689 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277689

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277689/0 /scratch/stefan/7808390/working/building/REAL300025277689 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/569
`/scratch/stefan/7808390/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277689 none CN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 32, 107, 107, 107, 107, 107, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 17, 17, 107, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 203
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: REAL300025277689 none CN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 6, 6, 13, 13, 13, 13, 13, 27, 27, 64, 106, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 64, 64, 201, 13, 13, 13] 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, 43, 44])
total number of confs: 479
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: REAL300025277689 none CN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 183, 183, 183, 107, 107, 107, 107, 107, 72, 41, 72, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 183, 107, 107, 107, 107, 107, 107, 41, 41, 1, 107, 107, 107] 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])
total number of confs: 593
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277689 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277689
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277689/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277689
Building REAL300025277690
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277690'
/scratch/stefan/7808390/working/building/REAL300025277690 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277690

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277690/0 /scratch/stefan/7808390/working/building/REAL300025277690 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/570
`/scratch/stefan/7808390/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=NC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277690 none O=C(CCN1C=NC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 8, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 29, 30, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 34, 34, 34, 34, 34, 1, 1, 29, 29, 30, 30, 37, 37, 6, 1, 1, 1, 1, 1, 1, 5, 5, 34, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277690 none O=C(CCN1C=NC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 8, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 8, 5, 1, 1, 1, 1, 1, 1, 14, 14, 37, 37, 37, 37, 37, 47, 47, 66, 106, 201, 201, 201, 201, 201, 37, 37, 8, 8, 5, 5, 1, 1, 14, 37, 37, 37, 37, 37, 37, 66, 66, 201, 37, 37, 37] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277690 none O=C(CCN1C=NC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 8, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [95, 95, 95, 201, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 21, 17, 21, 9, 1, 1, 1, 1, 1, 1, 1, 34, 34, 201, 201, 201, 201, 201, 201, 95, 34, 34, 34, 34, 34, 34, 17, 17, 1, 34, 34, 34] 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])
total number of confs: 730
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277690 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277690
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277690/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277690
Building REAL300025277691
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277691'
/scratch/stefan/7808390/working/building/REAL300025277691 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277691

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277691/0 /scratch/stefan/7808390/working/building/REAL300025277691 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/571
`/scratch/stefan/7808390/working/3D/571' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277691 none CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 77, 77, 77, 35, 35, 35, 35, 35, 28, 24, 28, 11, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 201, 201, 197, 197, 77, 35, 35, 35, 35, 35, 35, 24, 24, 1, 35, 35, 35] 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])
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: REAL300025277691 none CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 42, 36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 35, 35, 35, 35, 35, 1, 1, 49, 49, 49, 49, 49, 49, 49, 36, 36, 6, 1, 1, 1, 1, 1, 1, 5, 5, 35, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277691 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277691
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277691/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277691
Building REAL300025277692
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277692'
/scratch/stefan/7808390/working/building/REAL300025277692 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277692

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277692/0 /scratch/stefan/7808390/working/building/REAL300025277692 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/572
`/scratch/stefan/7808390/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277692 none CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 47, 121, 121, 121, 121, 121, 1, 1, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 27, 27, 121, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277692 none CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 32, 32, 103, 148, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 103, 103, 201, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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: 552
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277692 none CC1=CC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 121, 121, 121, 121, 121, 78, 43, 78, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 121, 43, 43, 1, 121, 121, 121] 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])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277692 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277692
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277692/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277692
Building REAL300025277693
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277693'
/scratch/stefan/7808390/working/building/REAL300025277693 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277693

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277693/0 /scratch/stefan/7808390/working/building/REAL300025277693 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/573
`/scratch/stefan/7808390/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277693 none CC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 102, 102, 102, 102, 102, 66, 53, 66, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 102, 102, 53, 53, 1, 102, 102, 102] 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])
total number of confs: 618
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277693 none CC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 16, 102, 102, 102, 102, 102, 1, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 9, 9, 102, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277693 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277693
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277693/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277693
Building REAL300025277694
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277694'
/scratch/stefan/7808390/working/building/REAL300025277694 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277694

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277694/0 /scratch/stefan/7808390/working/building/REAL300025277694 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/574
`/scratch/stefan/7808390/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277694 none O=C(CCN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 43, 43, 43, 43, 43, 1, 1, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 5, 5, 43, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 124
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277694 none O=C(CCN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 26, 26, 48, 87, 201, 201, 201, 201, 201, 15, 15, 3, 3, 3, 3, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 48, 48, 201, 15, 15, 15] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 491
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277694 none O=C(CCN1C=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [116, 116, 116, 201, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 27, 21, 27, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 201, 201, 116, 43, 43, 43, 43, 43, 43, 21, 21, 1, 43, 43, 43] 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])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277694 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277694
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277694/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277694
Building REAL300025277695
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277695'
/scratch/stefan/7808390/working/building/REAL300025277695 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277695

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277695/0 /scratch/stefan/7808390/working/building/REAL300025277695 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/575
`/scratch/stefan/7808390/working/3D/575' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3O)C2C1)

`REAL300025277695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277695 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3O)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 9, 16, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 11, 17, 17, 17, 1, 1, 9, 9, 63, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 34, 1, 1, 1] 402
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41])
total number of confs: 197
number of broken/clashed sets: 95
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277695 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3O)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 34, 13, 1, 1, 1, 1, 1, 1, 1, 43, 63, 63, 63, 63, 63, 137, 137, 137, 201, 201, 201, 201, 201, 201, 63, 63, 34, 34, 1, 63, 63, 63, 63, 63, 63, 137, 201, 201, 201, 201, 402, 63, 63, 63] 402
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: 930
number of broken/clashed sets: 95
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277695 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC=C3O)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 28, 66, 105, 201, 201, 201, 201, 201, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 66, 66, 201, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 2, 17, 17, 17] 402
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 503
number of broken/clashed sets: 95
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277695 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277695
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277695/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277695
Building REAL300025277696
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277696'
/scratch/stefan/7808390/working/building/REAL300025277696 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277696

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277696/0 /scratch/stefan/7808390/working/building/REAL300025277696 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/576
`/scratch/stefan/7808390/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277696 none CCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 123, 201, 123, 123, 55, 55, 55, 55, 55, 38, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 55, 55, 55, 55, 55, 55, 29, 29, 1, 55, 55, 55] 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])
total number of confs: 774
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277696 none CCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 55, 55, 55, 55, 55, 1, 1, 27, 27, 27, 27, 27, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 9, 9, 55, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277696 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277696
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277696/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277696
Building REAL300025277697
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277697'
/scratch/stefan/7808390/working/building/REAL300025277697 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277697

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277697/0 /scratch/stefan/7808390/working/building/REAL300025277697 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/577
`/scratch/stefan/7808390/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)SCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277697 none CC(C)SCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 195, 111, 111, 111, 48, 48, 48, 48, 48, 30, 28, 30, 12, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 201, 195, 195, 111, 48, 48, 48, 48, 48, 48, 28, 28, 1, 48, 48, 48] 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])
total number of confs: 780
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277697 none CC(C)SCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 48, 48, 48, 48, 48, 1, 1, 24, 24, 24, 24, 24, 24, 24, 19, 19, 6, 1, 1, 1, 1, 1, 1, 6, 6, 48, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277697 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277697
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277697/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277697
Building REAL300025277698
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277698'
/scratch/stefan/7808390/working/building/REAL300025277698 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277698

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277698/0 /scratch/stefan/7808390/working/building/REAL300025277698 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/578
`/scratch/stefan/7808390/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277698 none CC(=O)N(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 199, 201, 133, 133, 133, 54, 54, 54, 54, 54, 35, 26, 35, 11, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 201, 199, 199, 133, 54, 54, 54, 54, 54, 54, 26, 26, 1, 54, 54, 54] 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])
total number of confs: 755
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277698 none CC(=O)N(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 54, 54, 54, 54, 54, 1, 1, 35, 35, 35, 35, 35, 35, 32, 32, 6, 1, 1, 1, 1, 1, 1, 5, 5, 54, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 198
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277698 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277698
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277698/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277698
Building REAL300025277699
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277699'
/scratch/stefan/7808390/working/building/REAL300025277699 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277699

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277699/0 /scratch/stefan/7808390/working/building/REAL300025277699 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/579
`/scratch/stefan/7808390/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277699 none CCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 177, 198, 201, 177, 177, 72, 72, 72, 72, 72, 50, 36, 50, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 201, 198, 201, 201, 201, 201, 201, 177, 72, 72, 72, 72, 72, 72, 36, 36, 1, 72, 72, 72] 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])
total number of confs: 683
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277699 none CCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 6, 15, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 72, 72, 72, 72, 72, 1, 1, 20, 20, 20, 20, 20, 15, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 7, 7, 72, 1, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277699 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277699
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277699/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277699
Building REAL300025277700
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277700'
/scratch/stefan/7808390/working/building/REAL300025277700 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277700

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277700/0 /scratch/stefan/7808390/working/building/REAL300025277700 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/580
`/scratch/stefan/7808390/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277700 none CC(C)OCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 172, 201, 158, 158, 101, 101, 101, 34, 34, 34, 34, 34, 26, 22, 26, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 101, 34, 34, 34, 34, 34, 34, 22, 22, 1, 34, 34, 34] 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])
total number of confs: 792
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277700 none CC(C)OCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 20, 32, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 34, 34, 34, 34, 34, 1, 1, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 4, 4, 34, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277700 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277700
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277700/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277700
Building REAL300025277701
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277701'
/scratch/stefan/7808390/working/building/REAL300025277701 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277701

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277701/0 /scratch/stefan/7808390/working/building/REAL300025277701 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/581
`/scratch/stefan/7808390/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277701 none CCC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 78, 78, 78, 78, 78, 1, 1, 11, 26, 26, 26, 26, 26, 11, 6, 1, 1, 1, 1, 1, 1, 7, 7, 78, 1, 1, 1, 11] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277701 none CCC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 11, 11, 11, 11, 11, 16, 16, 33, 65, 167, 167, 167, 167, 167, 11, 11, 1, 7, 7, 7, 7, 7, 1, 4, 11, 11, 11, 11, 11, 11, 33, 33, 167, 11, 11, 11, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 46, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277701 none CCC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 165, 165, 165, 78, 78, 78, 78, 78, 51, 31, 51, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 167, 201, 201, 201, 201, 201, 167, 165, 78, 78, 78, 78, 78, 78, 31, 31, 1, 78, 78, 78, 167] 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: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277701 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277701
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277701/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277701
Building REAL300025277702
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277702'
/scratch/stefan/7808390/working/building/REAL300025277702 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277702

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277702/0 /scratch/stefan/7808390/working/building/REAL300025277702 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/582
`/scratch/stefan/7808390/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277702 none O=C(CCC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 27, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 66, 66, 66, 66, 66, 1, 1, 20, 20, 30, 30, 44, 44, 44, 44, 44, 44, 44, 4, 1, 1, 1, 1, 1, 1, 9, 9, 66, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277702 none O=C(CCC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 6, 1, 1, 1, 1, 1, 1, 29, 29, 44, 44, 44, 44, 44, 52, 52, 79, 114, 201, 201, 201, 201, 201, 44, 44, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 29, 44, 44, 44, 44, 44, 44, 79, 79, 201, 44, 44, 44] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 37, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 537
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277702 none O=C(CCC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 174, 185, 201, 201, 201, 201, 66, 66, 66, 66, 66, 55, 31, 55, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 174, 174, 197, 197, 201, 201, 201, 201, 201, 201, 201, 100, 66, 66, 66, 66, 66, 66, 31, 31, 1, 66, 66, 66] 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])
total number of confs: 895
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277702 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277702
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277702/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277702
Building REAL300025277703
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277703'
/scratch/stefan/7808390/working/building/REAL300025277703 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277703

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277703/0 /scratch/stefan/7808390/working/building/REAL300025277703 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/583
`/scratch/stefan/7808390/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3COCCO3)C2C1)

`REAL300025277703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277703 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3COCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 13, 25, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 1, 1, 13, 13, 95, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 45, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277703 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3COCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 37, 13, 1, 1, 1, 1, 1, 1, 1, 73, 95, 95, 95, 95, 95, 161, 161, 161, 201, 201, 201, 201, 201, 95, 95, 37, 37, 1, 95, 95, 95, 95, 95, 95, 161, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95] 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: 667
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277703 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3COCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 17, 30, 71, 114, 201, 201, 201, 201, 201, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 71, 71, 201, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 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, 35, 43, 44, 45])
total number of confs: 512
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277703 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277703
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277703/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277703
Building REAL300025277704
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277704'
/scratch/stefan/7808390/working/building/REAL300025277704 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277704

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277704/0 /scratch/stefan/7808390/working/building/REAL300025277704 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/584
`/scratch/stefan/7808390/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NN3)C2C1)

`REAL300025277704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277704 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [4, 1, 4, 18, 36, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 1, 1, 18, 18, 114, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277704 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [80, 47, 13, 1, 1, 1, 1, 1, 1, 1, 80, 114, 114, 114, 114, 114, 187, 187, 187, 201, 201, 201, 201, 114, 114, 47, 47, 1, 114, 114, 114, 114, 114, 114, 187, 201, 201, 201, 114, 114, 114] 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: 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: REAL300025277704 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [27, 15, 27, 75, 117, 201, 201, 201, 201, 201, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 15, 15, 75, 75, 201, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 15, 15, 15] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 478
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277704 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277704
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277704/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277704
Building REAL300025277705
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277705'
/scratch/stefan/7808390/working/building/REAL300025277705 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277705

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277705/0 /scratch/stefan/7808390/working/building/REAL300025277705 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/585
`/scratch/stefan/7808390/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=CC=N1)

`REAL300025277705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277705 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 159, 159, 67, 67, 67, 67, 67, 42, 31, 42, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 67, 67, 67, 67, 67, 67, 31, 31, 1, 67, 67, 67, 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])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277705 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 67, 67, 67, 67, 67, 1, 1, 18, 27, 27, 27, 27, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 6, 6, 67, 1, 1, 1, 27, 27, 27] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 43, 20, 21, 41, 36, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46])
total number of confs: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277705 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 8, 27, 27, 27, 27, 27, 39, 39, 63, 107, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 27, 27, 27, 27, 27, 27, 63, 63, 201, 27, 27, 27, 1, 1, 1] 201
rigid atoms, others: [1, 44, 45, 46, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 521
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277705 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277705
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277705/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277705
Building REAL300025277706
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277706'
/scratch/stefan/7808390/working/building/REAL300025277706 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277706

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277706/0 /scratch/stefan/7808390/working/building/REAL300025277706 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/586
`/scratch/stefan/7808390/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277706 none CCCCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 157, 87, 157, 157, 87, 87, 31, 31, 31, 31, 31, 22, 20, 22, 11, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 157, 87, 31, 31, 31, 31, 31, 31, 20, 20, 1, 31, 31, 31] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
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: REAL300025277706 none CCCCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 6, 6, 31, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277706 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277706
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277706/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277706
Building REAL300025277707
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277707'
/scratch/stefan/7808390/working/building/REAL300025277707 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277707

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277707/0 /scratch/stefan/7808390/working/building/REAL300025277707 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/587
`/scratch/stefan/7808390/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277707 none CSC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 194, 108, 194, 108, 108, 53, 53, 53, 53, 53, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 194, 194, 194, 194, 108, 53, 53, 53, 53, 53, 53, 29, 29, 1, 53, 53, 53] 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])
total number of confs: 799
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277707 none CSC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [34, 20, 6, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 53, 53, 53, 53, 53, 1, 1, 34, 34, 34, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 177
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277707 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277707
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277707/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277707
Building REAL300025277708
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277708'
/scratch/stefan/7808390/working/building/REAL300025277708 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277708

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277708/0 /scratch/stefan/7808390/working/building/REAL300025277708 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/588
`/scratch/stefan/7808390/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277708 none CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 151, 201, 151, 151, 75, 75, 75, 75, 75, 49, 31, 49, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 75, 75, 75, 75, 75, 75, 31, 31, 1, 75, 75, 75] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277708 none CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 6, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 75, 75, 75, 75, 75, 1, 1, 27, 27, 27, 27, 27, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 7, 7, 75, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277708 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277708
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277708/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277708
Building REAL300025277709
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277709'
/scratch/stefan/7808390/working/building/REAL300025277709 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277709

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277709/0 /scratch/stefan/7808390/working/building/REAL300025277709 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/589
`/scratch/stefan/7808390/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)COCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277709 none CC(C)COCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 195, 195, 114, 114, 114, 45, 45, 45, 45, 45, 30, 25, 30, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 114, 45, 45, 45, 45, 45, 45, 25, 25, 1, 45, 45, 45] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 759
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277709 none CC(C)COCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 33, 21, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 45, 45, 45, 45, 45, 1, 1, 33, 33, 33, 33, 33, 33, 33, 25, 25, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 5, 5, 45, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277709 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277709
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277709/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277709
Building REAL300025277710
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277710'
/scratch/stefan/7808390/working/building/REAL300025277710 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277710

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277710/0 /scratch/stefan/7808390/working/building/REAL300025277710 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/590
`/scratch/stefan/7808390/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277710 none CCOCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 195, 198, 101, 101, 101, 42, 42, 42, 42, 42, 29, 22, 29, 11, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 201, 201, 195, 201, 201, 201, 198, 198, 101, 42, 42, 42, 42, 42, 42, 22, 22, 1, 42, 42, 42] 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])
total number of confs: 776
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277710 none CCOCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 42, 42, 42, 42, 42, 1, 1, 32, 32, 32, 32, 32, 31, 31, 32, 32, 28, 28, 6, 1, 1, 1, 1, 1, 1, 5, 5, 42, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277710 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277710
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277710/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277710
Building REAL300025277711
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277711'
/scratch/stefan/7808390/working/building/REAL300025277711 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277711

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277711/0 /scratch/stefan/7808390/working/building/REAL300025277711 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/591
`/scratch/stefan/7808390/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277711 none O=C(COCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 17, 29, 43, 43, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 45, 45, 45, 45, 45, 1, 1, 10, 10, 29, 29, 43, 43, 43, 43, 43, 5, 1, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277711 none O=C(COCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 24, 13, 6, 1, 1, 1, 1, 26, 26, 43, 43, 43, 43, 43, 47, 47, 70, 102, 201, 201, 201, 201, 201, 43, 43, 24, 24, 6, 6, 1, 1, 1, 1, 1, 26, 43, 43, 43, 43, 43, 43, 70, 70, 201, 43, 43, 43] 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, 46, 47])
total number of confs: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277711 none O=C(COCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 146, 158, 180, 201, 201, 45, 45, 45, 45, 45, 35, 31, 35, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 146, 146, 180, 180, 201, 201, 201, 201, 201, 95, 45, 45, 45, 45, 45, 45, 31, 31, 1, 45, 45, 45] 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])
total number of confs: 772
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277711 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277711
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277711/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277711
Building REAL300025277712
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277712'
/scratch/stefan/7808390/working/building/REAL300025277712 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277712

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277712/0 /scratch/stefan/7808390/working/building/REAL300025277712 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/592
`/scratch/stefan/7808390/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277712 none O=C(CC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 51, 51, 51, 51, 51, 1, 1, 32, 32, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277712 none O=C(CC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 44, 44, 66, 112, 201, 201, 201, 201, 201, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 35, 35, 35, 66, 66, 201, 35, 35, 35] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 523
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277712 none O=C(CC1CCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 201, 201, 201, 201, 201, 51, 51, 51, 51, 51, 34, 27, 34, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 51, 51, 51, 51, 51, 51, 27, 27, 1, 51, 51, 51] 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])
total number of confs: 717
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277712 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277712
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277712/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277712
Building REAL300025277713
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277713'
/scratch/stefan/7808390/working/building/REAL300025277713 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277713

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277713/0 /scratch/stefan/7808390/working/building/REAL300025277713 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/593
`/scratch/stefan/7808390/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=N1)

`REAL300025277713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277713 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 58, 58, 58, 58, 58, 1, 1, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 9, 9, 58, 1, 1, 1, 22] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277713 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 22, 22, 22, 22, 22, 33, 33, 68, 104, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 68, 68, 201, 22, 22, 22, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 23, 24, 25] set([4, 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])
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: REAL300025277713 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 128, 128, 128, 58, 58, 58, 58, 58, 41, 35, 41, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 128, 58, 58, 58, 58, 58, 58, 35, 35, 1, 58, 58, 58, 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])
total number of confs: 511
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277713 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277713
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277713/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277713
Building REAL300025277714
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277714'
/scratch/stefan/7808390/working/building/REAL300025277714 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277714

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277714/0 /scratch/stefan/7808390/working/building/REAL300025277714 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/594
`/scratch/stefan/7808390/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNN=C3)C2C1)

`REAL300025277714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277714 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 23, 47, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 1, 1, 23, 23, 144, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
total number of confs: 265
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277714 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
0  hydrogens 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, 53, 13, 1, 1, 1, 1, 1, 1, 1, 97, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 144, 144, 53, 53, 1, 144, 144, 144, 144, 144, 144, 201, 201, 201, 201, 144, 144, 144] 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: 590
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277714 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 11, 25, 65, 111, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 65, 65, 201, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 469
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277714 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277714
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277714/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277714
Building REAL300025277715
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277715'
/scratch/stefan/7808390/working/building/REAL300025277715 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277715

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277715/0 /scratch/stefan/7808390/working/building/REAL300025277715 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/595
`/scratch/stefan/7808390/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CNC(=O)C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277715 none O=C(CNC(=O)C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 18, 18, 18, 37, 37, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 37, 37, 37, 37, 37, 1, 1, 18, 18, 18, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 1, 1, 4, 4, 37, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277715 none O=C(CNC(=O)C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 12, 12, 37, 37, 37, 37, 37, 49, 49, 69, 105, 201, 201, 201, 201, 201, 37, 37, 8, 8, 6, 1, 1, 1, 1, 1, 12, 37, 37, 37, 37, 37, 37, 69, 69, 201, 37, 37, 37] 201
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 30, 31] set([0, 1, 2, 3, 5, 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, 46, 47])
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: REAL300025277715 none O=C(CNC(=O)C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 148, 148, 148, 148, 201, 201, 37, 37, 37, 37, 37, 28, 23, 28, 11, 1, 1, 1, 1, 1, 1, 1, 37, 37, 148, 148, 148, 201, 201, 201, 201, 201, 91, 37, 37, 37, 37, 37, 37, 23, 23, 1, 37, 37, 37] 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])
total number of confs: 759
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277715 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277715
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277715/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277715
Building REAL300025277716
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277716'
/scratch/stefan/7808390/working/building/REAL300025277716 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277716

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277716/0 /scratch/stefan/7808390/working/building/REAL300025277716 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/596
`/scratch/stefan/7808390/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277716 none COCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 199, 127, 127, 127, 57, 57, 57, 57, 57, 38, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 193, 196, 201, 201, 199, 199, 127, 57, 57, 57, 57, 57, 57, 29, 29, 1, 57, 57, 57] 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])
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: REAL300025277716 none COCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 57, 57, 57, 57, 57, 1, 1, 31, 31, 31, 30, 29, 31, 31, 28, 28, 6, 1, 1, 1, 1, 1, 1, 5, 5, 57, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277716 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277716
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277716/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277716
Building REAL300025277717
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277717'
/scratch/stefan/7808390/working/building/REAL300025277717 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277717

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277717/0 /scratch/stefan/7808390/working/building/REAL300025277717 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/597
`/scratch/stefan/7808390/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277717 none O=C(COC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 31, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 41, 41, 41, 41, 41, 1, 1, 18, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 1, 1, 5, 5, 41, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277717 none O=C(COC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 4, 1, 1, 1, 1, 1, 1, 16, 16, 39, 39, 39, 39, 39, 45, 45, 65, 95, 201, 201, 201, 201, 201, 39, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 39, 39, 39, 39, 39, 39, 65, 65, 201, 39, 39, 39] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 37, 35, 36, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 489
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277717 none O=C(COC1CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 169, 175, 201, 201, 201, 201, 41, 41, 41, 41, 41, 33, 31, 33, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 41, 41, 41, 41, 41, 41, 31, 31, 1, 41, 41, 41] 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])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277717 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277717
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277717/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277717
Building REAL300025277718
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277718'
/scratch/stefan/7808390/working/building/REAL300025277718 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277718

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277718/0 /scratch/stefan/7808390/working/building/REAL300025277718 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/598
`/scratch/stefan/7808390/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277718 none CC1=NC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 5, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 15, 36, 36, 36, 36, 36, 1, 1, 18, 18, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 10, 10, 36, 1, 1, 1] 88
rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 44, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 117
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: REAL300025277718 none CC1=NC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 32, 32, 46, 63, 88, 88, 88, 88, 88, 18, 18, 2, 2, 2, 1, 1, 9, 18, 18, 18, 18, 18, 18, 46, 46, 88, 18, 18, 18] 88
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])
total number of confs: 250
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: REAL300025277718 none CC1=NC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 55, 88, 88, 55, 55, 55, 36, 36, 36, 36, 36, 33, 29, 33, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 88, 88, 88, 55, 88, 55, 36, 36, 36, 36, 36, 36, 29, 29, 1, 36, 36, 36] 88
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])
total number of confs: 327
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277718 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277718
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277718/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277718
Building REAL300025277719
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277719'
/scratch/stefan/7808390/working/building/REAL300025277719 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277719

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277719/0 /scratch/stefan/7808390/working/building/REAL300025277719 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/599
`/scratch/stefan/7808390/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277719 none CCSCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 179, 100, 100, 100, 46, 46, 46, 46, 46, 33, 27, 33, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 201, 201, 179, 179, 179, 179, 100, 46, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 46] 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])
total number of confs: 736
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277719 none CCSCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 51, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 46, 46, 46, 46, 46, 1, 1, 52, 52, 52, 52, 52, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277719 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277719
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277719/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277719
Building REAL300025277720
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277720'
/scratch/stefan/7808390/working/building/REAL300025277720 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277720

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277720/0 /scratch/stefan/7808390/working/building/REAL300025277720 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/600
`/scratch/stefan/7808390/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277720 none CCOC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 61, 61, 61, 61, 61, 1, 1, 36, 36, 36, 36, 36, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 5, 5, 61, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277720 none CCOC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 24, 24, 24, 24, 24, 35, 35, 59, 96, 193, 193, 193, 193, 193, 24, 24, 6, 6, 6, 6, 6, 1, 1, 1, 1, 7, 24, 24, 24, 24, 24, 24, 59, 59, 193, 24, 24, 24] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 496
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277720 none CCOC1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 193, 193, 136, 136, 136, 61, 61, 61, 61, 61, 41, 30, 41, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 193, 193, 193, 193, 136, 61, 61, 61, 61, 61, 61, 30, 30, 1, 61, 61, 61] 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])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277720 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277720
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277720/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277720
Building REAL300025277721
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277721'
/scratch/stefan/7808390/working/building/REAL300025277721 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277721

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277721/0 /scratch/stefan/7808390/working/building/REAL300025277721 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/601
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=NSN=C3)C2C1)

`REAL300025277721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277721 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', '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, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 22, 41, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 1, 1, 22, 22, 123, 1, 1, 1, 1, 1, 1, 6, 9, 1, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31] set([0, 35, 2, 3, 4, 5, 6, 7, 8, 9, 34, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27])
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: REAL300025277721 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', '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, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 49, 13, 1, 1, 1, 1, 1, 1, 1, 79, 123, 123, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123, 49, 49, 1, 123, 123, 123, 123, 123, 123, 201, 201, 123, 123, 123] 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: 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: REAL300025277721 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', '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, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 23, 71, 125, 201, 201, 201, 201, 201, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 71, 71, 201, 9, 9, 9, 9, 9, 9, 4, 1, 9, 9, 9] 201
rigid atoms, others: [35, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38])
total number of confs: 476
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277721 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277721
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277721/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277721
Building REAL300025277722
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277722'
/scratch/stefan/7808390/working/building/REAL300025277722 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277722

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277722/0 /scratch/stefan/7808390/working/building/REAL300025277722 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/602
`/scratch/stefan/7808390/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NS3)C2C1)

`REAL300025277722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277722 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.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, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 12, 22, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 1, 1, 12, 12, 85, 1, 1, 1, 1, 1, 1, 6, 16, 1, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31] set([0, 35, 2, 3, 4, 5, 6, 7, 8, 9, 34, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277722 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.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, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 42, 13, 1, 1, 1, 1, 1, 1, 1, 56, 85, 85, 85, 85, 85, 153, 153, 153, 201, 201, 201, 201, 85, 85, 42, 42, 1, 85, 85, 85, 85, 85, 85, 153, 201, 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])
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: REAL300025277722 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.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, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 16, 25, 66, 105, 201, 201, 201, 201, 201, 16, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 16, 16, 66, 66, 201, 16, 16, 16, 16, 16, 16, 7, 1, 16, 16, 16] 201
rigid atoms, others: [35, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38])
total number of confs: 481
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277722 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277722
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277722/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277722
Building REAL300025277723
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277723'
/scratch/stefan/7808390/working/building/REAL300025277723 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277723

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277723/0 /scratch/stefan/7808390/working/building/REAL300025277723 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/603
`/scratch/stefan/7808390/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277723 none COC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 183, 201, 174, 79, 79, 79, 36, 36, 36, 36, 36, 26, 22, 26, 10, 1, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 183, 174, 174, 79, 36, 36, 36, 36, 36, 36, 22, 22, 1, 36, 36, 36] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277723 none COC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [45, 45, 37, 45, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 36, 36, 36, 36, 36, 1, 1, 45, 45, 45, 37, 31, 31, 6, 1, 1, 1, 1, 1, 1, 4, 4, 36, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277723 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277723
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277723/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277723
Building REAL300025277724
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277724'
/scratch/stefan/7808390/working/building/REAL300025277724 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277724

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277724/0 /scratch/stefan/7808390/working/building/REAL300025277724 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/604
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=NOC=C3)C2C1)

`REAL300025277724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277724 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NOC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [5, 1, 5, 22, 45, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 1, 1, 22, 22, 126, 1, 1, 1, 1, 1, 1, 6, 7, 7, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
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: REAL300025277724 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NOC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [85, 47, 13, 1, 1, 1, 1, 1, 1, 1, 85, 126, 126, 126, 126, 126, 201, 201, 201, 201, 201, 201, 201, 126, 126, 47, 47, 1, 126, 126, 126, 126, 126, 126, 201, 201, 201, 126, 126, 126] 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: 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: REAL300025277724 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NOC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [17, 7, 17, 67, 118, 201, 201, 201, 201, 201, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 67, 67, 201, 7, 7, 7, 7, 7, 7, 3, 1, 1, 7, 7, 7] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 465
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277724 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277724
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277724/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277724
Building REAL300025277725
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277725'
/scratch/stefan/7808390/working/building/REAL300025277725 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277725

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277725/0 /scratch/stefan/7808390/working/building/REAL300025277725 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/605
`/scratch/stefan/7808390/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCSCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277725 none CCCSCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 141, 76, 76, 76, 30, 30, 30, 30, 30, 22, 21, 22, 13, 1, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 201, 201, 201, 201, 201, 141, 141, 76, 30, 30, 30, 30, 30, 30, 21, 21, 1, 30, 30, 30] 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])
total number of confs: 881
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277725 none CCCSCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 30, 30, 30, 30, 30, 1, 1, 33, 33, 33, 33, 33, 33, 33, 16, 16, 5, 1, 1, 1, 1, 1, 1, 6, 6, 30, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277725 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277725
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277725/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277725
Building REAL300025277726
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277726'
/scratch/stefan/7808390/working/building/REAL300025277726 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277726

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277726/0 /scratch/stefan/7808390/working/building/REAL300025277726 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/606
`/scratch/stefan/7808390/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277726 none CC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 81, 81, 81, 38, 38, 38, 38, 38, 29, 25, 29, 11, 1, 1, 1, 1, 1, 1, 1, 38, 38, 132, 201, 201, 132, 132, 132, 132, 81, 38, 38, 38, 38, 38, 38, 25, 25, 1, 38, 38, 38, 201, 201, 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, 47])
total number of confs: 713
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277726 none CC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 1, 1, 22, 41, 41, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1, 1, 41, 41, 41, 41, 41] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47])
total number of confs: 192
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277726 none CC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 13, 13, 13, 41, 41, 41, 41, 41, 52, 52, 78, 128, 201, 201, 201, 201, 201, 41, 41, 1, 1, 1, 3, 3, 3, 3, 13, 41, 41, 41, 41, 41, 41, 78, 78, 201, 41, 41, 41, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 43, 44, 45, 46, 47, 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, 22, 26, 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: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277726 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277726
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277726/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277726
Building REAL300025277727
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277727'
/scratch/stefan/7808390/working/building/REAL300025277727 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277727

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277727/0 /scratch/stefan/7808390/working/building/REAL300025277727 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/607
`/scratch/stefan/7808390/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277727 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 46, 127, 127, 127, 127, 127, 1, 1, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 26, 26, 127, 1, 1, 1, 16] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 264
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277727 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 16, 16, 16, 16, 16, 38, 38, 102, 144, 201, 201, 201, 201, 201, 16, 16, 1, 2, 2, 2, 1, 4, 16, 16, 16, 16, 16, 16, 102, 102, 201, 16, 16, 16, 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: 543
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277727 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 127, 127, 127, 127, 127, 78, 42, 78, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 127, 42, 42, 1, 127, 127, 127, 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])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277727 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277727
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277727/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277727
Building REAL300025277728
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277728'
/scratch/stefan/7808390/working/building/REAL300025277728 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277728

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277728/0 /scratch/stefan/7808390/working/building/REAL300025277728 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/608
`/scratch/stefan/7808390/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CS3)C2C1)

`REAL300025277728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277728 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 16, 28, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 1, 1, 16, 16, 97, 1, 1, 1, 1, 1, 1, 6, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277728 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 42, 13, 1, 1, 1, 1, 1, 1, 1, 63, 97, 97, 97, 97, 97, 171, 171, 171, 201, 201, 201, 201, 97, 97, 42, 42, 1, 97, 97, 97, 97, 97, 97, 171, 201, 201, 97, 97, 97] 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: 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: REAL300025277728 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 24, 68, 107, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 15, 15, 68, 68, 201, 15, 15, 15, 15, 15, 15, 6, 1, 1, 15, 15, 15] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 479
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277728 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277728
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277728/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277728
Building REAL300025277729
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277729'
/scratch/stefan/7808390/working/building/REAL300025277729 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277729

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277729/0 /scratch/stefan/7808390/working/building/REAL300025277729 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/609
`/scratch/stefan/7808390/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277729 none CC1=NN(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 28, 79, 79, 79, 79, 79, 1, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 17, 17, 79, 1, 1, 1, 18] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
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: REAL300025277729 none CC1=NN(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 18, 18, 18, 18, 18, 40, 40, 104, 142, 201, 201, 201, 201, 201, 18, 18, 1, 2, 2, 2, 2, 2, 2, 6, 18, 18, 18, 18, 18, 18, 104, 104, 201, 18, 18, 18, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 26] set([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])
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: REAL300025277729 none CC1=NN(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 131, 131, 131, 79, 79, 79, 79, 79, 53, 41, 53, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 201, 201, 201, 131, 79, 79, 79, 79, 79, 79, 41, 41, 1, 79, 79, 79, 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])
total number of confs: 548
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277729 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277729
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277729/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277729
Building REAL300025277730
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277730'
/scratch/stefan/7808390/working/building/REAL300025277730 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277730

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277730/0 /scratch/stefan/7808390/working/building/REAL300025277730 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/610
`/scratch/stefan/7808390/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=C1)

`REAL300025277730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277730 none CC1=CN(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 50, 50, 50, 50, 50, 1, 1, 25, 25, 25, 25, 25, 25, 22, 22, 6, 1, 1, 1, 1, 1, 1, 5, 5, 50, 1, 1, 1, 25] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 158
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277730 none CC1=CN(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 9, 9, 9, 25, 25, 25, 25, 25, 37, 37, 60, 103, 201, 201, 201, 201, 201, 25, 25, 1, 1, 2, 2, 2, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 60, 60, 201, 25, 25, 25, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 46, 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: 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: REAL300025277730 none CC1=CN(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 50, 50, 50, 50, 50, 33, 27, 33, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 121, 50, 50, 50, 50, 50, 50, 27, 27, 1, 50, 50, 50, 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])
total number of confs: 745
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277730 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277730
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277730/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277730
Building REAL300025277731
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277731'
/scratch/stefan/7808390/working/building/REAL300025277731 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277731

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277731/0 /scratch/stefan/7808390/working/building/REAL300025277731 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/611
`/scratch/stefan/7808390/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)COC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277731 none CC(C)COC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 192, 150, 192, 150, 150, 59, 59, 59, 59, 59, 40, 34, 40, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 150, 59, 59, 59, 59, 59, 59, 34, 34, 1, 59, 59, 59] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 711
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277731 none CC(C)COC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 18, 14, 6, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 59, 59, 59, 59, 59, 1, 1, 36, 36, 36, 36, 36, 36, 36, 24, 24, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 59, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277731 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277731
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277731/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277731
Building REAL300025277732
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277732'
/scratch/stefan/7808390/working/building/REAL300025277732 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277732

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277732/0 /scratch/stefan/7808390/working/building/REAL300025277732 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/612
`/scratch/stefan/7808390/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277732 none CCCC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 143, 143, 143, 143, 79, 79, 79, 31, 31, 31, 31, 31, 25, 22, 25, 10, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 79, 31, 31, 31, 31, 31, 31, 22, 22, 1, 31, 31, 31] 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])
total number of confs: 891
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277732 none CCCC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 31, 31, 31, 31, 31, 1, 1, 39, 39, 39, 39, 39, 39, 39, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 4, 4, 31, 1, 1, 1] 201
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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
/scratch/stefan/7808390/working/building/REAL300025277732 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277732
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277732/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277732
Building REAL300025277733
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277733'
/scratch/stefan/7808390/working/building/REAL300025277733 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277733

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277733/0 /scratch/stefan/7808390/working/building/REAL300025277733 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/613
`/scratch/stefan/7808390/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277733 none CCC=C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 109, 201, 109, 109, 43, 43, 43, 43, 43, 29, 22, 29, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 43, 43, 43, 43, 43, 43, 22, 22, 1, 43, 43, 43] 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])
total number of confs: 590
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277733 none CCC=C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 27, 6, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 43, 43, 43, 43, 43, 1, 1, 39, 39, 39, 39, 39, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 6, 6, 43, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 205
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277733 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277733
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277733/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277733
Building REAL300025277734
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277734'
/scratch/stefan/7808390/working/building/REAL300025277734 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277734

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277734/0 /scratch/stefan/7808390/working/building/REAL300025277734 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/614
`/scratch/stefan/7808390/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277734 none CS(=O)(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 148, 148, 148, 59, 59, 59, 59, 59, 38, 32, 38, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 148, 59, 59, 59, 59, 59, 59, 32, 32, 1, 59, 59, 59] 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])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277734 none CS(=O)(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 22, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 59, 59, 59, 59, 59, 1, 1, 27, 27, 27, 22, 22, 6, 1, 1, 1, 1, 1, 1, 6, 6, 59, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277734 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277734
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277734/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277734
Building REAL300025277735
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277735'
/scratch/stefan/7808390/working/building/REAL300025277735 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277735

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277735/0 /scratch/stefan/7808390/working/building/REAL300025277735 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/615
`/scratch/stefan/7808390/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277735 none O=C(C=C1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 27, 86, 86, 86, 86, 86, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 18, 18, 86, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277735 none O=C(C=C1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 19, 19, 19, 19, 19, 43, 43, 106, 140, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 19, 106, 106, 201, 19, 19, 19] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 33, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277735 none O=C(C=C1CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 156, 156, 201, 201, 201, 201, 201, 201, 86, 86, 86, 86, 86, 55, 39, 55, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 86, 86, 86, 86, 86, 86, 39, 39, 1, 86, 86, 86] 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])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277735 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277735
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277735/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277735
Building REAL300025277736
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277736'
/scratch/stefan/7808390/working/building/REAL300025277736 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277736

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277736/0 /scratch/stefan/7808390/working/building/REAL300025277736 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/616
`/scratch/stefan/7808390/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1)

`REAL300025277736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277736 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 21, 82, 82, 82, 82, 82, 1, 1, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 10, 10, 82, 1, 1, 1, 17] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277736 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 4, 4, 4, 17, 17, 17, 17, 17, 26, 26, 68, 113, 201, 201, 201, 201, 201, 17, 17, 1, 1, 1, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 68, 68, 201, 17, 17, 17, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 23, 24, 25] set([4, 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])
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: REAL300025277736 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 199, 199, 199, 82, 82, 82, 82, 82, 55, 40, 55, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 201, 201, 201, 201, 201, 201, 199, 82, 82, 82, 82, 82, 82, 40, 40, 1, 82, 82, 82, 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])
total number of confs: 595
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277736 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277736
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277736/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277736
Building REAL300025277737
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277737'
/scratch/stefan/7808390/working/building/REAL300025277737 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277737

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277737/0 /scratch/stefan/7808390/working/building/REAL300025277737 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/617
`/scratch/stefan/7808390/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277737 none CCOC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 201, 193, 158, 158, 68, 68, 68, 68, 68, 43, 35, 43, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 68, 68, 68, 68, 68, 68, 35, 35, 1, 68, 68, 68] 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])
total number of confs: 766
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277737 none CCOC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 6, 14, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 68, 68, 68, 68, 68, 1, 1, 15, 15, 15, 15, 15, 14, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 6, 6, 68, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277737 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277737
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277737/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277737
Building REAL300025277738
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277738'
/scratch/stefan/7808390/working/building/REAL300025277738 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277738

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277738/0 /scratch/stefan/7808390/working/building/REAL300025277738 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/618
`/scratch/stefan/7808390/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC(F)(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277738 none O=C(CC(F)(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 15, 15, 15, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 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: [109, 109, 109, 201, 201, 201, 201, 48, 48, 48, 48, 48, 33, 29, 33, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 109, 48, 48, 48, 48, 48, 48, 29, 29, 1, 48, 48, 48] 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])
total number of confs: 733
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277738 none O=C(CC(F)(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 5, 15, 15, 15, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 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: [6, 6, 6, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 48, 48, 48, 48, 48, 1, 1, 35, 35, 6, 1, 1, 1, 1, 1, 1, 9, 9, 48, 1, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 39, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277738 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277738
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277738/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277738
Building REAL300025277739
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277739'
/scratch/stefan/7808390/working/building/REAL300025277739 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277739

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277739/0 /scratch/stefan/7808390/working/building/REAL300025277739 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/619
`/scratch/stefan/7808390/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277739 none COC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 191, 201, 191, 191, 80, 80, 80, 80, 80, 49, 35, 49, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 191, 80, 80, 80, 80, 80, 80, 35, 35, 1, 80, 80, 80] 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])
total number of confs: 619
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277739 none COC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 22, 6, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 16, 80, 80, 80, 80, 80, 1, 1, 24, 24, 24, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 8, 8, 80, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277739 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277739
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277739/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277739
Building REAL300025277740
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277740'
/scratch/stefan/7808390/working/building/REAL300025277740 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277740

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277740/0 /scratch/stefan/7808390/working/building/REAL300025277740 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/620
`/scratch/stefan/7808390/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277740 none CC(C)OCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 173, 103, 103, 103, 51, 51, 51, 51, 51, 35, 31, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 173, 173, 103, 51, 51, 51, 51, 51, 51, 31, 31, 1, 51, 51, 51] 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])
total number of confs: 704
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277740 none CC(C)OCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 42, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 51, 51, 51, 51, 51, 1, 1, 42, 42, 42, 42, 42, 42, 42, 21, 21, 6, 1, 1, 1, 1, 1, 1, 6, 6, 51, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277740 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277740
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277740/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277740
Building REAL300025277741
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277741'
/scratch/stefan/7808390/working/building/REAL300025277741 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277741

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277741/0 /scratch/stefan/7808390/working/building/REAL300025277741 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/621
`/scratch/stefan/7808390/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OCC1CC1)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277741 none CC(OCC1CC1)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 14, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 41, 41, 41, 41, 41, 1, 1, 11, 11, 11, 11, 14, 14, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 6, 6, 41, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277741 none CC(OCC1CC1)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 7, 9, 9, 9, 24, 24, 24, 24, 24, 31, 31, 55, 85, 201, 201, 201, 201, 201, 24, 24, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 24, 24, 55, 55, 201, 24, 24, 24] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 35, 36, 37] set([0, 1, 2, 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, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277741 none CC(OCC1CC1)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 104, 123, 123, 148, 201, 201, 104, 104, 41, 41, 41, 41, 41, 28, 25, 28, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 123, 123, 123, 123, 148, 148, 201, 201, 201, 201, 201, 104, 41, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41, 41] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277741 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277741
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277741/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277741
Building REAL300025277742
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277742'
/scratch/stefan/7808390/working/building/REAL300025277742 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277742

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277742/0 /scratch/stefan/7808390/working/building/REAL300025277742 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/622
`/scratch/stefan/7808390/working/3D/622' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277742 none CCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 108, 108, 108, 46, 46, 46, 46, 46, 36, 32, 36, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 186, 186, 108, 46, 46, 46, 46, 46, 46, 32, 32, 1, 46, 46, 46] 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])
total number of confs: 722
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277742 none CCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 23, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 46, 46, 46, 46, 46, 1, 1, 51, 51, 51, 51, 51, 28, 28, 13, 13, 6, 1, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 264
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277742 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277742
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277742/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277742
Building REAL300025277743
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277743'
/scratch/stefan/7808390/working/building/REAL300025277743 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277743

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277743/0 /scratch/stefan/7808390/working/building/REAL300025277743 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/623
`/scratch/stefan/7808390/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277743 none CCCCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 96, 95, 95, 87, 95, 87, 87, 33, 33, 33, 33, 33, 25, 22, 25, 11, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 201, 201, 96, 96, 95, 95, 95, 95, 87, 33, 33, 33, 33, 33, 33, 22, 22, 1, 33, 33, 33] 201
rigid atoms, others: [49, 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, 50, 51, 52])
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: REAL300025277743 none CCCCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 9, 9, 6, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 33, 33, 33, 33, 33, 1, 1, 24, 24, 24, 24, 24, 24, 24, 10, 10, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 6, 6, 33, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277743 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277743
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277743/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277743
Building REAL300025277744
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277744'
/scratch/stefan/7808390/working/building/REAL300025277744 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277744

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277744/0 /scratch/stefan/7808390/working/building/REAL300025277744 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/624
`/scratch/stefan/7808390/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277744 none C=CCCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 115, 112, 112, 100, 112, 100, 100, 37, 37, 37, 37, 37, 25, 22, 25, 11, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 115, 115, 112, 112, 112, 112, 100, 37, 37, 37, 37, 37, 37, 22, 22, 1, 37, 37, 37] 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])
total number of confs: 801
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277744 none C=CCCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 13, 9, 9, 6, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 37, 37, 37, 37, 37, 1, 1, 28, 28, 28, 24, 24, 13, 13, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 6, 6, 37, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277744 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277744
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277744/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277744
Building REAL300025277745
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277745'
/scratch/stefan/7808390/working/building/REAL300025277745 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277745

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277745/0 /scratch/stefan/7808390/working/building/REAL300025277745 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/625
`/scratch/stefan/7808390/working/3D/625' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOC3)C2C1)

`REAL300025277745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277745 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 9, 15, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 1, 1, 9, 9, 62, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 23, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277745 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 37, 13, 1, 1, 1, 1, 1, 1, 1, 43, 62, 62, 62, 62, 62, 120, 120, 120, 201, 201, 201, 201, 62, 62, 37, 37, 1, 62, 62, 62, 62, 62, 62, 120, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62] 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: 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: REAL300025277745 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 28, 39, 75, 113, 201, 201, 201, 201, 201, 28, 28, 28, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 28, 28, 75, 75, 201, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44])
total number of confs: 514
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277745 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277745
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277745/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277745
Building REAL300025277746
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277746'
/scratch/stefan/7808390/working/building/REAL300025277746 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277746

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277746/0 /scratch/stefan/7808390/working/building/REAL300025277746 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/626
`/scratch/stefan/7808390/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC(F)=C3)C2C1)

`REAL300025277746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277746 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 17, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 10, 10, 47, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277746 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 27, 12, 1, 1, 1, 1, 1, 1, 1, 31, 47, 47, 47, 47, 47, 71, 71, 71, 201, 201, 201, 201, 201, 201, 47, 47, 27, 27, 1, 47, 47, 47, 47, 47, 47, 71, 201, 201, 201, 47, 47, 47] 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: 413
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277746 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 20, 36, 69, 114, 201, 201, 201, 201, 201, 20, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 20, 20, 69, 69, 201, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 503
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277746 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277746
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277746/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277746
Building REAL300025277747
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277747'
/scratch/stefan/7808390/working/building/REAL300025277747 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277747

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277747/0 /scratch/stefan/7808390/working/building/REAL300025277747 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/627
`/scratch/stefan/7808390/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1)

`REAL300025277747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277747 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 43, 121, 121, 121, 121, 121, 1, 1, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 25, 25, 121, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39])
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: REAL300025277747 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 21, 21, 21, 21, 21, 44, 44, 108, 146, 201, 201, 201, 201, 201, 21, 21, 1, 2, 2, 2, 1, 7, 21, 21, 21, 21, 21, 21, 108, 108, 201, 21, 21, 21] 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])
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: REAL300025277747 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)S1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 194, 194, 194, 121, 121, 121, 121, 121, 73, 43, 73, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 194, 121, 121, 121, 121, 121, 121, 43, 43, 1, 121, 121, 121] 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])
total number of confs: 620
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277747 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277747
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277747/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277747
Building REAL300025277748
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277748'
/scratch/stefan/7808390/working/building/REAL300025277748 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277748

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277748/0 /scratch/stefan/7808390/working/building/REAL300025277748 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/628
`/scratch/stefan/7808390/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277748 none CN1N=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 35, 112, 112, 112, 112, 112, 1, 1, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 20, 20, 112, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 215
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277748 none CN1N=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 14, 14, 14, 14, 14, 30, 30, 71, 115, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 14, 71, 71, 201, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 490
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: REAL300025277748 none CN1N=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 190, 190, 190, 112, 112, 112, 112, 112, 71, 41, 71, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 190, 112, 112, 112, 112, 112, 112, 41, 41, 1, 112, 112, 112] 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])
total number of confs: 599
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277748 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277748
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277748/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277748
Building REAL300025277749
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277749'
/scratch/stefan/7808390/working/building/REAL300025277749 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277749

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277749/0 /scratch/stefan/7808390/working/building/REAL300025277749 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/629
`/scratch/stefan/7808390/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277749 none CCC(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [185, 201, 135, 201, 201, 135, 135, 57, 57, 57, 57, 57, 37, 30, 37, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 57, 57, 57, 57, 57, 57, 30, 30, 1, 57, 57, 57] 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])
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: REAL300025277749 none CCC(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 15, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 57, 57, 57, 57, 57, 1, 1, 27, 27, 27, 27, 27, 15, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 6, 6, 57, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277749 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277749
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277749/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277749
Building REAL300025277750
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277750'
/scratch/stefan/7808390/working/building/REAL300025277750 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277750

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277750/0 /scratch/stefan/7808390/working/building/REAL300025277750 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/630
`/scratch/stefan/7808390/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277750 none COCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 193, 161, 73, 73, 73, 35, 35, 35, 35, 35, 26, 23, 26, 11, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 193, 193, 193, 193, 161, 161, 73, 35, 35, 35, 35, 35, 35, 23, 23, 1, 35, 35, 35] 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])
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: REAL300025277750 none COCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 30, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 35, 35, 35, 35, 35, 1, 1, 32, 32, 32, 32, 32, 30, 30, 30, 30, 22, 22, 5, 1, 1, 1, 1, 1, 1, 4, 4, 35, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277750 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277750
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277750/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277750
Building REAL300025277751
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277751'
/scratch/stefan/7808390/working/building/REAL300025277751 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277751

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277751/0 /scratch/stefan/7808390/working/building/REAL300025277751 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/631
`/scratch/stefan/7808390/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277751 none CCCC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 185, 201, 64, 64, 64, 31, 31, 31, 31, 31, 23, 22, 23, 11, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 64, 31, 31, 31, 31, 31, 31, 22, 22, 1, 31, 31, 31] 201
rigid atoms, others: [48, 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, 49, 50, 51])
total number of confs: 754
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277751 none CCCC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 32, 42, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 31, 31, 31, 31, 31, 1, 1, 52, 52, 52, 52, 52, 52, 52, 42, 42, 42, 42, 32, 32, 6, 1, 1, 1, 1, 1, 1, 4, 4, 31, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277751 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277751
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277751/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277751
Building REAL300025277752
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277752'
/scratch/stefan/7808390/working/building/REAL300025277752 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277752

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277752/0 /scratch/stefan/7808390/working/building/REAL300025277752 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/632
`/scratch/stefan/7808390/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277752 none COC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 200, 127, 127, 127, 61, 61, 61, 61, 61, 38, 31, 38, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 200, 200, 127, 61, 61, 61, 61, 61, 61, 31, 31, 1, 61, 61, 61] 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])
total number of confs: 712
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277752 none COC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 33, 39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 61, 61, 61, 61, 61, 1, 1, 43, 43, 43, 41, 41, 41, 41, 33, 33, 6, 1, 1, 1, 1, 1, 1, 6, 6, 61, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 259
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277752 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277752
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277752/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277752
Building REAL300025277753
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277753'
/scratch/stefan/7808390/working/building/REAL300025277753 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277753

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277753/0 /scratch/stefan/7808390/working/building/REAL300025277753 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/633
`/scratch/stefan/7808390/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1)

`REAL300025277753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277753 none CN1C=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 13, 38, 38, 38, 38, 38, 1, 1, 51, 51, 51, 51, 51, 51, 19, 19, 6, 1, 1, 1, 1, 1, 1, 9, 9, 38, 1, 1, 1, 51] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277753 none CN1C=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 13, 13, 13, 51, 51, 51, 51, 51, 72, 72, 102, 151, 201, 201, 201, 201, 201, 51, 51, 1, 1, 2, 2, 2, 1, 7, 7, 13, 51, 51, 51, 51, 51, 51, 102, 102, 201, 51, 51, 51, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 46, 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: 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: REAL300025277753 none CN1C=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 80, 80, 80, 38, 38, 38, 38, 38, 25, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 38, 38, 201, 201, 201, 201, 201, 201, 144, 144, 80, 38, 38, 38, 38, 38, 38, 25, 25, 1, 38, 38, 38, 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])
total number of confs: 662
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277753 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277753
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277753/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277753
Building REAL300025277754
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277754'
/scratch/stefan/7808390/working/building/REAL300025277754 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277754

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277754/0 /scratch/stefan/7808390/working/building/REAL300025277754 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/634
`/scratch/stefan/7808390/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCCC3)C2C1)

`REAL300025277754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277754 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 18, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 20, 1, 1, 10, 10, 64, 1, 1, 1, 1, 1, 1, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 50, 51, 52, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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, 49])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277754 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 64, 64, 64, 64, 112, 112, 112, 201, 201, 201, 201, 201, 201, 64, 64, 29, 29, 1, 64, 64, 64, 64, 64, 64, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64] 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: 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: REAL300025277754 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 30, 68, 103, 201, 201, 201, 201, 201, 20, 20, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 20, 20, 68, 68, 201, 20, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [48, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 50, 51, 52])
total number of confs: 510
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277754 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277754
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277754/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277754
Building REAL300025277755
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277755'
/scratch/stefan/7808390/working/building/REAL300025277755 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277755

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277755/0 /scratch/stefan/7808390/working/building/REAL300025277755 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/635
`/scratch/stefan/7808390/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277755 none C=CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 124, 124, 124, 62, 62, 62, 62, 62, 38, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 124, 62, 62, 62, 62, 62, 62, 29, 29, 1, 62, 62, 62] 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])
total number of confs: 771
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277755 none C=CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [50, 34, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 62, 62, 62, 62, 62, 1, 1, 50, 50, 50, 34, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 5, 62, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 264
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277755 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277755
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277755/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277755
Building REAL300025277756
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277756'
/scratch/stefan/7808390/working/building/REAL300025277756 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277756

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277756/0 /scratch/stefan/7808390/working/building/REAL300025277756 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/636
`/scratch/stefan/7808390/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCC3)C2C1)

`REAL300025277756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277756 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 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]
0  hydrogens need 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, 9, 14, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 1, 1, 9, 9, 62, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 45, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 138
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277756 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 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]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 44, 62, 62, 62, 62, 62, 118, 118, 118, 201, 201, 201, 201, 201, 62, 62, 38, 38, 1, 62, 62, 62, 62, 62, 62, 118, 201, 201, 201, 201, 201, 201, 201, 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, 42, 43, 44, 45])
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: REAL300025277756 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 28, 40, 74, 113, 201, 201, 201, 201, 201, 28, 28, 28, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 74, 74, 201, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 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, 35, 43, 44, 45])
total number of confs: 505
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277756 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277756
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277756/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277756
Building REAL300025277757
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277757'
/scratch/stefan/7808390/working/building/REAL300025277757 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277757

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277757/0 /scratch/stefan/7808390/working/building/REAL300025277757 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/637
`/scratch/stefan/7808390/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277757 none COC(=O)C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [34, 34, 26, 34, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 19, 55, 55, 55, 55, 55, 1, 1, 34, 34, 34, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 14, 14, 55, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 200
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277757 none COC(=O)C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 46, 46, 99, 139, 196, 196, 196, 196, 196, 26, 26, 3, 3, 3, 1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 99, 99, 196, 26, 26, 26] 201
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 30, 31] set([0, 1, 3, 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: 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: REAL300025277757 none COC(=O)C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 196, 201, 196, 196, 115, 115, 115, 55, 55, 55, 55, 55, 34, 30, 34, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 196, 196, 196, 196, 115, 55, 55, 55, 55, 55, 55, 30, 30, 1, 55, 55, 55] 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])
total number of confs: 603
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277757 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277757
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277757/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277757
Building REAL300025277758
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277758'
/scratch/stefan/7808390/working/building/REAL300025277758 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277758

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277758/0 /scratch/stefan/7808390/working/building/REAL300025277758 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/638
`/scratch/stefan/7808390/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOC3)C2C1)

`REAL300025277758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277758 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7]
0  hydrogens need 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, 12, 22, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 1, 1, 12, 12, 87, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 191
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: REAL300025277758 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 68, 87, 87, 87, 87, 87, 135, 135, 135, 201, 201, 201, 201, 201, 87, 87, 39, 39, 1, 87, 87, 87, 87, 87, 87, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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, 42, 43, 44, 45, 46, 47])
total number of confs: 675
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: REAL300025277758 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 23, 38, 73, 115, 201, 201, 201, 201, 201, 23, 23, 23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 73, 73, 201, 23, 23, 23, 23, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 35, 45, 46, 47])
total number of confs: 509
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277758 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277758
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277758/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277758
Building REAL300025277759
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277759'
/scratch/stefan/7808390/working/building/REAL300025277759 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277759

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277759/0 /scratch/stefan/7808390/working/building/REAL300025277759 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/639
`/scratch/stefan/7808390/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277759 none CCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 50, 50, 50, 50, 50, 34, 26, 34, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 50, 50, 50, 50, 50, 50, 26, 26, 1, 50, 50, 50] 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])
total number of confs: 732
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277759 none CCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 50, 50, 50, 50, 50, 1, 1, 32, 32, 32, 32, 32, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 5, 5, 50, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277759 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277759
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277759/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277759
Building REAL300025277760
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277760'
/scratch/stefan/7808390/working/building/REAL300025277760 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277760

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277760/0 /scratch/stefan/7808390/working/building/REAL300025277760 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/640
`/scratch/stefan/7808390/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277760 none CCNC(=O)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 196, 187, 196, 187, 93, 93, 93, 39, 39, 39, 39, 39, 27, 23, 27, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 196, 187, 187, 187, 187, 93, 39, 39, 39, 39, 39, 39, 23, 23, 1, 39, 39, 39] 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])
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: REAL300025277760 none CCNC(=O)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 31, 20, 31, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 39, 39, 39, 39, 39, 1, 1, 42, 42, 42, 42, 42, 31, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 5, 5, 39, 1, 1, 1] 201
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277760 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277760
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277760/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277760
Building REAL300025277761
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277761'
/scratch/stefan/7808390/working/building/REAL300025277761 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277761

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277761/0 /scratch/stefan/7808390/working/building/REAL300025277761 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/641
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CSC=N3)C2C1)

`REAL300025277761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277761 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 39, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 1, 1, 19, 19, 124, 1, 1, 1, 1, 1, 1, 6, 11, 11, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277761 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 49, 13, 1, 1, 1, 1, 1, 1, 1, 78, 124, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 124, 124, 49, 49, 1, 124, 124, 124, 124, 124, 124, 201, 201, 201, 124, 124, 124] 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: 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: REAL300025277761 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 73, 121, 201, 201, 201, 201, 201, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 73, 73, 201, 11, 11, 11, 11, 11, 11, 4, 1, 1, 11, 11, 11] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277761 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277761
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277761/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277761
Building REAL300025277762
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277762'
/scratch/stefan/7808390/working/building/REAL300025277762 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277762

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277762/0 /scratch/stefan/7808390/working/building/REAL300025277762 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/642
`/scratch/stefan/7808390/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277762 none COCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 126, 201, 126, 126, 64, 64, 64, 64, 64, 43, 35, 43, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 64, 64, 64, 64, 64, 64, 35, 35, 1, 64, 64, 64] 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])
total number of confs: 777
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277762 none COCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 64, 64, 64, 64, 64, 1, 1, 40, 40, 40, 30, 30, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 64, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277762 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277762
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277762/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277762
Building REAL300025277763
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277763'
/scratch/stefan/7808390/working/building/REAL300025277763 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277763

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277763/0 /scratch/stefan/7808390/working/building/REAL300025277763 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/643
`/scratch/stefan/7808390/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277763 none CC(C)(C)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 186, 194, 73, 73, 73, 35, 35, 35, 35, 35, 24, 22, 24, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 73, 35, 35, 35, 35, 35, 35, 22, 22, 1, 35, 35, 35] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 971
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277763 none CC(C)(C)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 48, 40, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 35, 35, 35, 35, 35, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 35, 5, 1, 1, 1, 1, 1, 1, 4, 4, 35, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277763 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277763
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277763/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277763
Building REAL300025277764
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277764'
/scratch/stefan/7808390/working/building/REAL300025277764 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277764

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277764/0 /scratch/stefan/7808390/working/building/REAL300025277764 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/644
`/scratch/stefan/7808390/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277764 none C=CCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 177, 172, 118, 118, 118, 54, 54, 54, 54, 54, 37, 31, 37, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 172, 172, 118, 54, 54, 54, 54, 54, 54, 31, 31, 1, 54, 54, 54] 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])
total number of confs: 752
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277764 none C=CCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 29, 17, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 54, 54, 54, 54, 54, 1, 1, 35, 35, 35, 29, 29, 11, 11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277764 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277764
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277764/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277764
Building REAL300025277765
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277765'
/scratch/stefan/7808390/working/building/REAL300025277765 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277765

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277765/0 /scratch/stefan/7808390/working/building/REAL300025277765 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/645
`/scratch/stefan/7808390/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=N3)C2C1)

`REAL300025277765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277765 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [5, 1, 5, 22, 42, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 1, 1, 22, 22, 124, 1, 1, 1, 1, 1, 1, 6, 7, 7, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
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: REAL300025277765 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [84, 46, 13, 1, 1, 1, 1, 1, 1, 1, 84, 124, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 124, 124, 46, 46, 1, 124, 124, 124, 124, 124, 124, 201, 201, 201, 124, 124, 124] 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: 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: REAL300025277765 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=COC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [17, 7, 17, 67, 119, 201, 201, 201, 201, 201, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 67, 67, 201, 7, 7, 7, 7, 7, 7, 3, 1, 1, 7, 7, 7] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/7808390/working/building/REAL300025277765 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277765
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277765/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277765
Building REAL300025277766
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277766'
/scratch/stefan/7808390/working/building/REAL300025277766 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277766

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277766/0 /scratch/stefan/7808390/working/building/REAL300025277766 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/646
`/scratch/stefan/7808390/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCC(=O)N3)C2C1)

`REAL300025277766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277766 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 10, 20, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 1, 1, 10, 10, 78, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 24, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277766 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 38, 12, 1, 1, 1, 1, 1, 1, 1, 52, 78, 78, 78, 78, 78, 180, 180, 180, 201, 201, 201, 201, 201, 201, 78, 78, 38, 38, 1, 78, 78, 78, 78, 78, 78, 180, 201, 201, 201, 201, 201, 78, 78, 78] 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: 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: REAL300025277766 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 24, 33, 75, 111, 201, 201, 201, 201, 201, 24, 24, 24, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 24, 24, 75, 75, 201, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 24, 24, 24] 201
rigid atoms, others: [37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 502
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277766 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277766
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277766/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277766
Building REAL300025277767
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277767'
/scratch/stefan/7808390/working/building/REAL300025277767 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277767

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277767/0 /scratch/stefan/7808390/working/building/REAL300025277767 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/647
`/scratch/stefan/7808390/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277767 none O=C(CC1=CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 48, 48, 48, 48, 48, 1, 1, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 1, 1, 1, 1, 1, 1, 5, 5, 48, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277767 none O=C(CC1=CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 44, 44, 44, 44, 44, 56, 56, 76, 114, 201, 201, 201, 201, 201, 44, 44, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 44, 44, 44, 44, 44, 44, 76, 76, 201, 44, 44, 44] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277767 none O=C(CC1=CCCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 199, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 32, 26, 32, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 48, 48, 48, 48, 48, 48, 26, 26, 1, 48, 48, 48] 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])
total number of confs: 739
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277767 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277767
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277767/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277767
Building REAL300025277768
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277768'
/scratch/stefan/7808390/working/building/REAL300025277768 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277768

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277768/0 /scratch/stefan/7808390/working/building/REAL300025277768 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/648
`/scratch/stefan/7808390/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1)

`REAL300025277768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277768 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 44, 118, 118, 118, 118, 118, 1, 1, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 26, 26, 118, 1, 1, 1, 17] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277768 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 4, 4, 4, 17, 17, 17, 17, 17, 42, 42, 108, 148, 201, 201, 201, 201, 201, 17, 17, 1, 2, 2, 2, 1, 4, 17, 17, 17, 17, 17, 17, 108, 108, 201, 17, 17, 17, 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: 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: REAL300025277768 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 196, 196, 196, 118, 118, 118, 118, 118, 72, 41, 72, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 196, 118, 118, 118, 118, 118, 118, 41, 41, 1, 118, 118, 118, 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])
total number of confs: 631
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277768 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277768
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277768/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277768
Building REAL300025277769
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277769'
/scratch/stefan/7808390/working/building/REAL300025277769 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277769

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277769/0 /scratch/stefan/7808390/working/building/REAL300025277769 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/649
`/scratch/stefan/7808390/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277769 none CSCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 181, 105, 181, 105, 105, 46, 46, 46, 46, 46, 34, 30, 34, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 182, 182, 181, 181, 181, 181, 105, 46, 46, 46, 46, 46, 46, 30, 30, 1, 46, 46, 46] 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])
total number of confs: 744
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277769 none CSCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 29, 24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 46, 46, 46, 46, 46, 1, 1, 50, 50, 50, 29, 29, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 6, 6, 46, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277769 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277769
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277769/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277769
Building REAL300025277770
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277770'
/scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277770

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277770/0 /scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/650
`/scratch/stefan/7808390/working/3D/650' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277770 none C[N@@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 1, 1, 1] 6
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 25
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277770 none C[N@@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 5, 5, 6, 4, 4, 4] 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])
total number of confs: 25
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277770 none C[N@@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5] 6
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])
total number of confs: 15
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277770/1 /scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/651
`/scratch/stefan/7808390/working/3D/651' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277770.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277770/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277770 none C[N@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 8, 1, 1, 1] 8
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 30
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277770 none C[N@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 8, 8, 8, 8, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 6, 8, 4, 4, 4] 8
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])
total number of confs: 28
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: REAL300025277770 none C[N@H+]1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 8, 8, 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, 8, 8, 1, 8, 8, 8] 8
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])
total number of confs: 9
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277770/2 /scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/652
`/scratch/stefan/7808390/working/3D/652' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277770.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277770/2/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: REAL300025277770 none CN1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 40, 136, 136, 136, 136, 136, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 21, 21, 136, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
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: REAL300025277770 none CN1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 2, 6, 6, 6, 6, 6, 18, 18, 55, 104, 201, 201, 201, 201, 201, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 55, 55, 201, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 33, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277770 none CN1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 136, 88, 50, 88, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 136, 136, 136, 136, 50, 50, 1, 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])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277770 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277770
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277770/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277770/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277770/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277770
Building REAL300025277771
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277771'
/scratch/stefan/7808390/working/building/REAL300025277771 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277771

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277771/0 /scratch/stefan/7808390/working/building/REAL300025277771 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/653
`/scratch/stefan/7808390/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277771 none CCC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 144, 144, 144, 144, 92, 92, 92, 41, 41, 41, 41, 41, 30, 25, 30, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 144, 144, 144, 92, 41, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41, 41] 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])
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: REAL300025277771 none CCC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 41, 41, 41, 41, 41, 1, 1, 48, 48, 48, 48, 48, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 5, 5, 41, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 258
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277771 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277771
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277771/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277771
Building REAL300025277772
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277772'
/scratch/stefan/7808390/working/building/REAL300025277772 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277772

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277772/0 /scratch/stefan/7808390/working/building/REAL300025277772 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/654
`/scratch/stefan/7808390/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277772 none CC(C)(C)C=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 117, 117, 117, 51, 51, 51, 51, 51, 34, 30, 34, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 51, 51, 51, 51, 51, 51, 30, 30, 1, 51, 51, 51] 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])
total number of confs: 614
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277772 none CC(C)(C)C=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 18, 51, 51, 51, 51, 51, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 12, 12, 51, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277772 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277772
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277772/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277772
Building REAL300025277773
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277773'
/scratch/stefan/7808390/working/building/REAL300025277773 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277773

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277773/0 /scratch/stefan/7808390/working/building/REAL300025277773 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/655
`/scratch/stefan/7808390/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)N=C3)C2C1)

`REAL300025277773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277773 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)N=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 31, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 1, 17, 17, 107, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 197
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: REAL300025277773 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)N=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 47, 13, 1, 1, 1, 1, 1, 1, 1, 77, 107, 107, 107, 107, 107, 172, 172, 172, 201, 201, 201, 201, 201, 201, 107, 107, 47, 47, 1, 107, 107, 107, 107, 107, 107, 172, 201, 201, 201, 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])
total number of confs: 591
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: REAL300025277773 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)N=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 66, 104, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 66, 66, 201, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 483
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277773 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277773
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277773/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277773
Building REAL300025277774
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277774'
/scratch/stefan/7808390/working/building/REAL300025277774 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277774

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277774/0 /scratch/stefan/7808390/working/building/REAL300025277774 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/656
`/scratch/stefan/7808390/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277774 none COCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 164, 157, 90, 90, 90, 45, 45, 45, 45, 45, 32, 28, 32, 11, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 193, 193, 157, 157, 90, 45, 45, 45, 45, 45, 45, 28, 28, 1, 45, 45, 45] 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])
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: REAL300025277774 none COCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 23, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 45, 45, 45, 45, 45, 1, 1, 33, 33, 33, 33, 33, 29, 29, 14, 14, 5, 1, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277774 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277774
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277774/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277774
Building REAL300025277775
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277775'
/scratch/stefan/7808390/working/building/REAL300025277775 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277775

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277775/0 /scratch/stefan/7808390/working/building/REAL300025277775 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/657
`/scratch/stefan/7808390/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277775 none CCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 100, 180, 100, 100, 43, 43, 43, 43, 43, 29, 25, 29, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 100, 43, 43, 43, 43, 43, 43, 25, 25, 1, 43, 43, 43] 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])
total number of confs: 805
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277775 none CCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 43, 43, 43, 43, 43, 1, 1, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 5, 5, 43, 1, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277775 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277775
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277775/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277775
Building REAL300025277776
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277776'
/scratch/stefan/7808390/working/building/REAL300025277776 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277776

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277776/0 /scratch/stefan/7808390/working/building/REAL300025277776 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/658
`/scratch/stefan/7808390/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277776 none CC1=NN(C)C=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 44, 113, 113, 113, 113, 113, 1, 1, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 27, 27, 113, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277776 none CC1=NN(C)C=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 8, 8, 8, 21, 21, 21, 21, 21, 44, 44, 115, 154, 201, 201, 201, 201, 201, 21, 21, 2, 2, 2, 2, 2, 2, 1, 8, 21, 21, 21, 21, 21, 21, 115, 115, 201, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277776 none CC1=NN(C)C=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 113, 113, 113, 113, 113, 79, 43, 79, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 197, 113, 113, 113, 113, 113, 113, 43, 43, 1, 113, 113, 113] 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])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277776 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277776
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277776/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277776
Building REAL300025277777
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277777'
/scratch/stefan/7808390/working/building/REAL300025277777 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277777

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277777/0 /scratch/stefan/7808390/working/building/REAL300025277777 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/659
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CC4CCC3O4)C2C1)

`REAL300025277777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277777 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4CCC3O4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [3, 1, 3, 15, 29, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1, 15, 15, 100, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 46, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277777 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4CCC3O4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [69, 41, 13, 1, 1, 1, 1, 1, 1, 1, 69, 100, 100, 100, 100, 100, 185, 185, 185, 201, 201, 201, 201, 201, 201, 100, 100, 41, 41, 1, 100, 100, 100, 100, 100, 100, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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, 48])
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: REAL300025277777 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4CCC3O4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [25, 14, 25, 67, 109, 201, 201, 201, 201, 201, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 67, 67, 201, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48])
total number of confs: 476
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277777 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277777
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277777/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277777
Building REAL300025277778
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277778'
/scratch/stefan/7808390/working/building/REAL300025277778 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277778

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277778/0 /scratch/stefan/7808390/working/building/REAL300025277778 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/660
`/scratch/stefan/7808390/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1)

`REAL300025277778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277778 none CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 90, 90, 90, 90, 90, 1, 1, 33, 33, 33, 33, 33, 33, 19, 19, 4, 1, 1, 1, 1, 1, 1, 12, 12, 90, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277778 none CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 9, 25, 25, 25, 33, 33, 33, 33, 33, 45, 45, 69, 108, 201, 201, 201, 201, 201, 33, 33, 1, 1, 2, 2, 2, 1, 9, 9, 25, 33, 33, 33, 33, 33, 33, 69, 69, 201, 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: 512
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277778 none CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 189, 114, 114, 114, 90, 90, 90, 90, 90, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 201, 201, 201, 189, 189, 114, 90, 90, 90, 90, 90, 90, 29, 29, 1, 90, 90, 90] 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])
total number of confs: 697
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277778 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277778
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277778/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277778
Building REAL300025277779
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277779'
/scratch/stefan/7808390/working/building/REAL300025277779 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277779

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277779/0 /scratch/stefan/7808390/working/building/REAL300025277779 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/661
`/scratch/stefan/7808390/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=N1)

`REAL300025277779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277779 none CCN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 90, 90, 90, 90, 90, 1, 1, 10, 10, 28, 28, 28, 28, 28, 10, 5, 1, 1, 1, 1, 1, 1, 11, 11, 90, 1, 1, 1, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 236
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: REAL300025277779 none CCN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 10, 10, 10, 10, 10, 19, 19, 41, 64, 161, 161, 161, 161, 161, 10, 10, 1, 1, 7, 7, 7, 7, 7, 1, 5, 10, 10, 10, 10, 10, 10, 41, 41, 161, 10, 10, 10, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 46, 25, 26] set([0, 6, 7, 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, 44, 45])
total number of confs: 365
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: REAL300025277779 none CCN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 161, 161, 161, 136, 136, 136, 90, 90, 90, 90, 90, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 161, 161, 201, 201, 201, 201, 201, 161, 136, 90, 90, 90, 90, 90, 90, 30, 30, 1, 90, 90, 90, 161] 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: 699
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277779 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277779
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277779/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277779
Building REAL300025277780
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277780'
/scratch/stefan/7808390/working/building/REAL300025277780 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277780

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277780/0 /scratch/stefan/7808390/working/building/REAL300025277780 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/662
`/scratch/stefan/7808390/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277780 none NC1=NC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [14, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 46, 118, 118, 118, 118, 118, 1, 1, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 26, 26, 118, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 43, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277780 none NC1=NC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 4, 4, 14, 14, 14, 14, 14, 38, 38, 109, 150, 201, 201, 201, 201, 201, 14, 14, 2, 2, 1, 1, 4, 14, 14, 14, 14, 14, 14, 109, 109, 201, 14, 14, 14] 201
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: 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: REAL300025277780 none NC1=NC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 118, 118, 118, 118, 118, 79, 43, 79, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 118, 43, 43, 1, 118, 118, 118] 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])
total number of confs: 647
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277780 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277780
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277780/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277780
Building REAL300025277781
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277781'
/scratch/stefan/7808390/working/building/REAL300025277781 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277781

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277781/0 /scratch/stefan/7808390/working/building/REAL300025277781 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/663
`/scratch/stefan/7808390/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277781 none O=C(CCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 38, 60, 60, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 35, 35, 35, 35, 35, 1, 1, 35, 35, 38, 38, 60, 60, 60, 60, 60, 5, 1, 1, 1, 1, 1, 1, 4, 4, 35, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 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: REAL300025277781 none O=C(CCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 21, 60, 60, 60, 60, 60, 71, 71, 97, 132, 201, 201, 201, 201, 201, 60, 60, 7, 7, 3, 3, 1, 1, 1, 1, 1, 21, 60, 60, 60, 60, 60, 60, 97, 97, 201, 60, 60, 60] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 29, 30, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277781 none O=C(CCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 184, 186, 201, 201, 35, 35, 35, 35, 35, 25, 23, 25, 11, 1, 1, 1, 1, 1, 1, 1, 35, 35, 184, 184, 186, 186, 201, 201, 201, 201, 201, 78, 35, 35, 35, 35, 35, 35, 23, 23, 1, 35, 35, 35] 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])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277781 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277781
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277781/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277781
Building REAL300025277782
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277782'
/scratch/stefan/7808390/working/building/REAL300025277782 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277782

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277782/0 /scratch/stefan/7808390/working/building/REAL300025277782 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/664
`/scratch/stefan/7808390/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1)

`REAL300025277782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277782 none CC1=C(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 38, 103, 103, 103, 103, 103, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 24, 24, 103, 1, 1, 1, 16] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277782 none CC1=C(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 16, 16, 16, 16, 16, 40, 40, 109, 150, 201, 201, 201, 201, 201, 16, 16, 1, 1, 2, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 16, 16, 109, 109, 201, 16, 16, 16, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 26] set([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])
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: REAL300025277782 none CC1=C(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 103, 103, 103, 103, 103, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 199, 103, 103, 103, 103, 103, 103, 38, 38, 1, 103, 103, 103, 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])
total number of confs: 615
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277782 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277782/1 /scratch/stefan/7808390/working/building/REAL300025277782 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/665
`/scratch/stefan/7808390/working/3D/665' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1C)

`REAL300025277782.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277782/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277782 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1C 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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 18, 48, 48, 48, 48, 48, 1, 1, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 14, 14, 48, 1, 1, 1, 29, 29, 29] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46])
total number of confs: 136
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: REAL300025277782 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1C 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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 29, 29, 29, 29, 29, 46, 46, 105, 138, 201, 201, 201, 201, 201, 29, 29, 1, 1, 2, 2, 2, 1, 9, 29, 29, 29, 29, 29, 29, 105, 105, 201, 29, 29, 29, 2, 2, 2] 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, 46])
total number of confs: 604
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: REAL300025277782 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1C 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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 109, 109, 109, 48, 48, 48, 48, 48, 32, 30, 32, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 109, 48, 48, 48, 48, 48, 48, 30, 30, 1, 48, 48, 48, 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])
total number of confs: 471
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277782 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277782
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277782/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277782/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277782
Building REAL300025277783
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277783'
/scratch/stefan/7808390/working/building/REAL300025277783 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277783

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277783/0 /scratch/stefan/7808390/working/building/REAL300025277783 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/666
`/scratch/stefan/7808390/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277783 none O=C(CC1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 30, 30, 30, 30, 30, 1, 1, 38, 38, 54, 54, 54, 54, 54, 54, 54, 54, 54, 6, 1, 1, 1, 1, 1, 1, 4, 4, 30, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277783 none O=C(CC1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 54, 54, 54, 54, 54, 65, 65, 87, 116, 201, 201, 201, 201, 201, 54, 54, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 54, 54, 54, 54, 54, 54, 87, 87, 201, 54, 54, 54] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277783 none O=C(CC1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 198, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 21, 19, 21, 9, 1, 1, 1, 1, 1, 1, 1, 30, 30, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 30, 30, 30, 30, 30, 30, 19, 19, 1, 30, 30, 30] 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])
total number of confs: 766
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277783 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277783
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277783/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277783
Building REAL300025277784
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277784'
/scratch/stefan/7808390/working/building/REAL300025277784 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277784

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277784/0 /scratch/stefan/7808390/working/building/REAL300025277784 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/667
`/scratch/stefan/7808390/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277784 none CCCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 109, 109, 104, 64, 64, 64, 37, 37, 37, 37, 37, 31, 29, 31, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 201, 201, 109, 109, 104, 104, 64, 37, 37, 37, 37, 37, 37, 29, 29, 1, 37, 37, 37] 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])
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: REAL300025277784 none CCCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 16, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 37, 37, 37, 37, 37, 1, 1, 33, 33, 33, 33, 33, 33, 33, 17, 17, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 37, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277784 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277784
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277784/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277784
Building REAL300025277785
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277785'
/scratch/stefan/7808390/working/building/REAL300025277785 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277785

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277785/0 /scratch/stefan/7808390/working/building/REAL300025277785 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/668
`/scratch/stefan/7808390/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277785 none O=C(CC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 12, 1, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 29, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 52, 52, 52, 52, 52, 1, 1, 29, 29, 33, 33, 6, 1, 1, 1, 1, 1, 1, 5, 5, 52, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277785 none O=C(CC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 12, 1, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 48, 48, 68, 112, 201, 201, 201, 201, 201, 33, 33, 4, 4, 1, 1, 11, 33, 33, 33, 33, 33, 33, 68, 68, 201, 33, 33, 33] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29] set([0, 1, 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: 524
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277785 none O=C(CC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 8, 12, 1, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 201, 201, 201, 201, 201, 52, 52, 52, 52, 52, 34, 27, 34, 11, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 135, 52, 52, 52, 52, 52, 52, 27, 27, 1, 52, 52, 52] 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])
total number of confs: 788
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277785 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277785
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277785/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277785
Building REAL300025277786
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277786'
/scratch/stefan/7808390/working/building/REAL300025277786 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277786

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277786/0 /scratch/stefan/7808390/working/building/REAL300025277786 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/669
`/scratch/stefan/7808390/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1)

`REAL300025277786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277786 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [22, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 16, 87, 87, 87, 87, 87, 1, 1, 12, 12, 12, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 8, 8, 87, 1, 1, 1, 12] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277786 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 20, 20, 40, 67, 187, 187, 187, 187, 187, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 40, 40, 187, 12, 12, 12, 1] 201
rigid atoms, others: [1, 2, 3, 4, 45, 24, 25, 26] set([0, 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])
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: REAL300025277786 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 187, 187, 165, 165, 165, 87, 87, 87, 87, 87, 52, 31, 52, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 187, 187, 187, 201, 201, 201, 201, 201, 165, 87, 87, 87, 87, 87, 87, 31, 31, 1, 87, 87, 87, 187] 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: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277786 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277786
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277786/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277786
Building REAL300025277787
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277787'
/scratch/stefan/7808390/working/building/REAL300025277787 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277787

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277787/0 /scratch/stefan/7808390/working/building/REAL300025277787 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/670
`/scratch/stefan/7808390/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277787 none O=C(CC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 11, 51, 51, 51, 51, 51, 1, 1, 24, 24, 43, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 1, 1, 1, 8, 8, 51, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
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: REAL300025277787 none O=C(CC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 5, 1, 1, 1, 1, 1, 1, 23, 23, 43, 43, 43, 43, 43, 59, 59, 91, 124, 201, 201, 201, 201, 201, 43, 43, 5, 5, 1, 1, 1, 1, 1, 1, 1, 23, 43, 43, 43, 43, 43, 43, 91, 91, 201, 43, 43, 43] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277787 none O=C(CC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 195, 201, 201, 201, 201, 51, 51, 51, 51, 51, 42, 29, 42, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 195, 195, 201, 201, 201, 201, 201, 201, 201, 94, 51, 51, 51, 51, 51, 51, 29, 29, 1, 51, 51, 51] 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])
total number of confs: 777
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277787 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277787
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277787/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277787
Building REAL300025277788
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277788'
/scratch/stefan/7808390/working/building/REAL300025277788 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277788

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277788/0 /scratch/stefan/7808390/working/building/REAL300025277788 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/671
`/scratch/stefan/7808390/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CC3)C2C1)

`REAL300025277788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277788 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 8, 13, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 1, 1, 8, 8, 48, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 23, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277788 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 33, 13, 1, 1, 1, 1, 1, 1, 1, 37, 48, 48, 48, 48, 48, 99, 99, 99, 201, 201, 201, 201, 48, 48, 33, 33, 1, 48, 48, 48, 48, 48, 48, 99, 201, 201, 201, 201, 201, 201, 201, 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, 39, 40, 41, 42, 43, 44])
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: REAL300025277788 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC=CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 30, 37, 74, 114, 201, 201, 201, 201, 201, 30, 30, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 30, 30, 74, 74, 201, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44])
total number of confs: 504
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277788 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277788
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277788/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277788
Building REAL300025277789
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277789'
/scratch/stefan/7808390/working/building/REAL300025277789 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277789

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277789/0 /scratch/stefan/7808390/working/building/REAL300025277789 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/672
`/scratch/stefan/7808390/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=NNC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277789 none O=C(CC1=NNC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 26, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 61, 61, 61, 61, 61, 1, 1, 26, 26, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 5, 5, 61, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 189
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277789 none O=C(CC1=NNC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 44, 44, 65, 107, 201, 201, 201, 201, 201, 33, 33, 5, 5, 1, 1, 1, 12, 33, 33, 33, 33, 33, 33, 65, 65, 201, 33, 33, 33] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025277789 none O=C(CC1=NNC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 8, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [149, 149, 149, 201, 201, 201, 201, 201, 61, 61, 61, 61, 61, 39, 30, 39, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 149, 61, 61, 61, 61, 61, 61, 30, 30, 1, 61, 61, 61] 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])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277789 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277789
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277789/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277789
Building REAL300025277790
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277790'
/scratch/stefan/7808390/working/building/REAL300025277790 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277790

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277790/0 /scratch/stefan/7808390/working/building/REAL300025277790 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/673
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=NC=C3F)C2C1)

`REAL300025277790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277790 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 24, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 8, 15, 15, 15, 1, 1, 12, 12, 97, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277790 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 42, 13, 1, 1, 1, 1, 1, 1, 1, 60, 97, 97, 97, 97, 97, 195, 195, 195, 201, 201, 201, 201, 201, 201, 97, 97, 42, 42, 1, 97, 97, 97, 97, 97, 97, 195, 201, 201, 201, 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])
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: REAL300025277790 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 15, 27, 66, 107, 201, 201, 201, 201, 201, 15, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 66, 66, 201, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 15, 15, 15] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 477
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277790 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277790
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277790/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277790
Building REAL300025277791
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277791'
/scratch/stefan/7808390/working/building/REAL300025277791 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277791

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277791/0 /scratch/stefan/7808390/working/building/REAL300025277791 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/674
`/scratch/stefan/7808390/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=NN1C)

`REAL300025277791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277791 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 33, 95, 95, 95, 95, 95, 1, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 19, 19, 95, 1, 1, 1, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277791 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 19, 19, 19, 19, 19, 49, 49, 122, 150, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 122, 122, 201, 19, 19, 19, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26] set([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, 42, 43, 44, 45])
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: REAL300025277791 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 183, 95, 95, 95, 95, 95, 59, 38, 59, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 201, 183, 95, 95, 95, 95, 95, 95, 38, 38, 1, 95, 95, 95, 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])
total number of confs: 589
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277791 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277791
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277791/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277791
Building REAL300025277792
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277792'
/scratch/stefan/7808390/working/building/REAL300025277792 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277792

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277792/0 /scratch/stefan/7808390/working/building/REAL300025277792 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/675
`/scratch/stefan/7808390/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277792 none CC1=CC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 16, 48, 48, 48, 48, 48, 1, 1, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 1, 1, 12, 12, 48, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 138
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277792 none CC1=CC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 9, 9, 9, 35, 35, 35, 35, 35, 53, 53, 113, 144, 201, 201, 201, 201, 201, 35, 35, 2, 2, 2, 1, 1, 1, 9, 35, 35, 35, 35, 35, 35, 113, 113, 201, 35, 35, 35] 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: 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: REAL300025277792 none CC1=CC=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 107, 107, 107, 48, 48, 48, 48, 48, 29, 29, 29, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 107, 48, 48, 48, 48, 48, 48, 29, 29, 1, 48, 48, 48] 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])
total number of confs: 456
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277792 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277792
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277792/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277792
Building REAL300025277793
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277793'
/scratch/stefan/7808390/working/building/REAL300025277793 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277793

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277793/0 /scratch/stefan/7808390/working/building/REAL300025277793 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/676
`/scratch/stefan/7808390/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277793 none CC1=CN=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 18, 61, 61, 61, 61, 61, 1, 1, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 9, 9, 61, 1, 1, 1, 19] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
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: REAL300025277793 none CC1=CN=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 5, 5, 19, 19, 19, 19, 19, 31, 31, 69, 104, 201, 201, 201, 201, 201, 19, 19, 1, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 19, 19, 69, 69, 201, 19, 19, 19, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 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])
total number of confs: 508
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277793 none CC1=CN=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 94, 94, 94, 61, 61, 61, 61, 61, 40, 33, 40, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 94, 61, 61, 61, 61, 61, 61, 33, 33, 1, 61, 61, 61, 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])
total number of confs: 459
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277793 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277793
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277793/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277793
Building REAL300025277794
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277794'
/scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025277794

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277794/0 /scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/677
`/scratch/stefan/7808390/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277794 none CN1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 32, 32, 32, 32, 32, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 10, 10, 32, 1, 1, 1, 13, 13] 52
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 48, 49])
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: REAL300025277794 none CN1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 13, 13, 19, 19, 30, 42, 52, 52, 52, 52, 52, 13, 13, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 30, 30, 52, 13, 13, 13, 1, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 48, 49, 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, 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.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277794 none CN1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 43, 43, 43, 32, 32, 32, 32, 32, 25, 22, 25, 10, 1, 1, 1, 1, 1, 1, 1, 32, 32, 52, 52, 52, 52, 52, 52, 52, 52, 52, 43, 32, 32, 32, 32, 32, 32, 22, 22, 1, 32, 32, 32, 52, 52] 52
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, 49])
total number of confs: 171
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277794/1 /scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/678
`/scratch/stefan/7808390/working/3D/678' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277794.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277794/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277794 none C[N@@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 4, 4, 6, 1, 1, 1, 5, 5] 6
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50])
total number of confs: 35
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277794 none C[N@@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 2, 2, 2, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 1, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 49, 50, 35, 33, 27, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 23
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: REAL300025277794 none C[N@@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 5, 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, 1, 6, 6, 6, 6, 6] 6
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, 50])
total number of confs: 12
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025277794/2 /scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/679
`/scratch/stefan/7808390/working/3D/679' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277794.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025277794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277794/2/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: REAL300025277794 none C[N@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 20, 51, 51, 51, 51, 51, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 15, 15, 51, 1, 1, 1, 11, 11] 98
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277794 none C[N@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 25, 25, 52, 67, 98, 98, 98, 98, 98, 11, 11, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 11, 11, 52, 52, 98, 11, 11, 11, 1, 1] 98
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 49, 50, 35, 33, 27, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277794 none C[N@H+]1CCOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 98, 98, 51, 51, 51, 51, 51, 39, 31, 39, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 51, 51, 51, 51, 51, 51, 31, 31, 1, 51, 51, 51, 98, 98] 98
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, 50])
total number of confs: 292
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277794 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277794
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025277794/2.*
1: /scratch/stefan/7808390/working/building/REAL300025277794/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277794/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277794
Building REAL300025277795
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277795'
/scratch/stefan/7808390/working/building/REAL300025277795 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277795

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277795/0 /scratch/stefan/7808390/working/building/REAL300025277795 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/680
`/scratch/stefan/7808390/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277795 none CC1=NC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 91, 91, 91, 91, 91, 1, 1, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 18, 18, 91, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277795 none CC1=NC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 50, 50, 111, 146, 201, 201, 201, 201, 201, 21, 21, 1, 2, 2, 2, 2, 2, 2, 5, 21, 21, 21, 21, 21, 21, 111, 111, 201, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([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])
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: REAL300025277795 none CC1=NC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 194, 194, 194, 91, 91, 91, 91, 91, 57, 38, 57, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 194, 91, 91, 91, 91, 91, 91, 38, 38, 1, 91, 91, 91] 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])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277795 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277795
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277795/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277795
Building REAL300025277796
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277796'
/scratch/stefan/7808390/working/building/REAL300025277796 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277796

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277796/0 /scratch/stefan/7808390/working/building/REAL300025277796 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/681
`/scratch/stefan/7808390/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC(F)(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277796 none O=C(CCC(F)(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 15, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [95, 95, 95, 187, 201, 201, 201, 201, 41, 41, 41, 41, 41, 29, 26, 29, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 187, 187, 201, 201, 95, 41, 41, 41, 41, 41, 41, 26, 26, 1, 41, 41, 41] 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])
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: REAL300025277796 none O=C(CCC(F)(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 15, 15, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 34, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 10, 41, 41, 41, 41, 41, 1, 1, 34, 34, 41, 41, 6, 1, 1, 1, 1, 1, 1, 7, 7, 41, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277796 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277796
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277796/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277796
Building REAL300025277797
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277797'
/scratch/stefan/7808390/working/building/REAL300025277797 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277797

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277797/0 /scratch/stefan/7808390/working/building/REAL300025277797 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/682
`/scratch/stefan/7808390/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277797 none C=CCOCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 184, 184, 184, 110, 110, 110, 40, 40, 40, 40, 40, 28, 21, 28, 11, 1, 1, 1, 1, 1, 1, 1, 40, 40, 201, 201, 201, 201, 201, 184, 184, 184, 184, 184, 184, 110, 40, 40, 40, 40, 40, 40, 21, 21, 1, 40, 40, 40] 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])
total number of confs: 818
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277797 none C=CCOCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 40, 40, 40, 40, 40, 1, 1, 26, 26, 26, 21, 21, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 7, 7, 40, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 174
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277797 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277797
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277797/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277797
Building REAL300025277798
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277798'
/scratch/stefan/7808390/working/building/REAL300025277798 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277798

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277798/0 /scratch/stefan/7808390/working/building/REAL300025277798 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/683
`/scratch/stefan/7808390/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277798 none O=C(CC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 64, 64, 64, 64, 64, 1, 1, 20, 20, 41, 41, 41, 41, 41, 41, 41, 4, 1, 1, 1, 1, 1, 1, 7, 7, 64, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277798 none O=C(CC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 1, 1, 1, 1, 1, 26, 26, 41, 41, 41, 41, 41, 58, 58, 96, 133, 201, 201, 201, 201, 201, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 96, 96, 201, 41, 41, 41] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 27, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277798 none O=C(CC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 163, 201, 201, 201, 64, 64, 64, 64, 64, 52, 31, 52, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 163, 163, 201, 201, 201, 201, 201, 201, 201, 99, 64, 64, 64, 64, 64, 64, 31, 31, 1, 64, 64, 64] 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])
total number of confs: 824
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277798 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277798
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277798/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277798
Building REAL300025277799
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277799'
/scratch/stefan/7808390/working/building/REAL300025277799 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277799

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277799/0 /scratch/stefan/7808390/working/building/REAL300025277799 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/684
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=CC(=O)N3)C2C1)

`REAL300025277799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277799 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [2, 1, 2, 8, 13, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 1, 1, 8, 8, 49, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277799 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [33, 29, 13, 1, 1, 1, 1, 1, 1, 1, 33, 49, 49, 49, 49, 49, 86, 86, 86, 201, 201, 201, 201, 201, 201, 49, 49, 29, 29, 1, 49, 49, 49, 49, 49, 49, 86, 201, 201, 201, 201, 49, 49, 49] 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: 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: REAL300025277799 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [36, 27, 36, 75, 114, 201, 201, 201, 201, 201, 27, 27, 27, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 27, 27, 75, 75, 201, 27, 27, 27, 27, 27, 27, 8, 1, 1, 1, 1, 27, 27, 27] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 523
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277799 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277799
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277799/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277799
Building REAL300025277800
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277800'
/scratch/stefan/7808390/working/building/REAL300025277800 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277800

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277800/0 /scratch/stefan/7808390/working/building/REAL300025277800 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/685
`/scratch/stefan/7808390/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1(C)C)

`REAL300025277800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277800 none CC1(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1(C)C 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 20, 93, 93, 93, 93, 93, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 11, 11, 93, 1, 1, 1, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 46, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50, 51, 52])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277800 none CC1(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1(C)C 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 12, 12, 12, 12, 12, 24, 24, 57, 94, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 12, 12, 12, 12, 12, 12, 57, 57, 201, 12, 12, 12, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 47, 48, 49, 24, 25, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52])
total number of confs: 480
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277800 none CC1(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1(C)C 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 93, 93, 93, 93, 93, 66, 52, 66, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 93, 93, 93, 93, 93, 93, 52, 52, 1, 93, 93, 93, 201, 201, 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, 52])
total number of confs: 683
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277800 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277800
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277800/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277800
Building REAL300025277801
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277801'
/scratch/stefan/7808390/working/building/REAL300025277801 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277801

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277801/0 /scratch/stefan/7808390/working/building/REAL300025277801 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/686
`/scratch/stefan/7808390/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=N1)

`REAL300025277801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277801 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 22, 84, 84, 84, 84, 84, 1, 1, 18, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 10, 10, 84, 1, 1, 1, 19] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42])
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: REAL300025277801 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 28, 28, 70, 113, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 2, 2, 2, 6, 19, 19, 19, 19, 19, 19, 70, 70, 201, 19, 19, 19, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 23, 24, 25] set([4, 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])
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: REAL300025277801 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)OC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 182, 182, 182, 84, 84, 84, 84, 84, 58, 43, 58, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 182, 84, 84, 84, 84, 84, 84, 43, 43, 1, 84, 84, 84, 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])
total number of confs: 584
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277801 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277801
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277801/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277801
Building REAL300025277802
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277802'
/scratch/stefan/7808390/working/building/REAL300025277802 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277802

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277802/0 /scratch/stefan/7808390/working/building/REAL300025277802 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/687
`/scratch/stefan/7808390/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277802 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 116, 116, 116, 51, 51, 51, 51, 51, 35, 29, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 116, 51, 51, 51, 51, 51, 51, 29, 29, 1, 51, 51, 51, 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])
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: REAL300025277802 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 51, 51, 51, 51, 51, 1, 1, 34, 35, 35, 34, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 6, 6, 51, 1, 1, 1, 35, 35, 35, 35, 35] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21, 41, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43, 44, 45, 46])
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: REAL300025277802 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 35, 35, 35, 35, 35, 46, 46, 75, 117, 201, 201, 201, 201, 201, 35, 35, 1, 1, 1, 2, 2, 2, 2, 13, 35, 35, 35, 35, 35, 35, 75, 75, 201, 35, 35, 35, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 46, 22, 23, 24] set([0, 2, 3, 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, 38, 39, 40, 41])
total number of confs: 529
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277802 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277802
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277802/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277802
Building REAL300025277803
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277803'
/scratch/stefan/7808390/working/building/REAL300025277803 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277803

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277803/0 /scratch/stefan/7808390/working/building/REAL300025277803 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/688
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3C4CCCC43)C2C1)

`REAL300025277803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277803 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C4CCCC43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 15, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 32, 32, 32, 32, 1, 1, 10, 10, 54, 1, 1, 1, 1, 1, 1, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 168
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277803 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C4CCCC43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 12, 1, 1, 1, 1, 1, 1, 1, 39, 54, 54, 54, 54, 54, 93, 93, 93, 201, 201, 201, 201, 201, 54, 54, 32, 32, 1, 54, 54, 54, 54, 54, 54, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 54, 54] 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: 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: REAL300025277803 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C4CCCC43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 77, 116, 201, 201, 201, 201, 201, 32, 32, 32, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 32, 32, 77, 77, 201, 32, 32, 32, 32, 32, 32, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 35, 45, 46, 47])
total number of confs: 506
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277803 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277803
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277803/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277803
Building REAL300025277804
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277804'
/scratch/stefan/7808390/working/building/REAL300025277804 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277804

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277804/0 /scratch/stefan/7808390/working/building/REAL300025277804 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/689
`/scratch/stefan/7808390/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277804 none N#CC1=CNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 37, 106, 106, 106, 106, 106, 1, 1, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 23, 23, 106, 1, 1, 1, 20] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 36, 37, 38, 42])
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: REAL300025277804 none N#CC1=CNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 20, 20, 20, 20, 20, 49, 49, 110, 144, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 4, 20, 20, 20, 20, 20, 20, 110, 110, 201, 20, 20, 20, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 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: REAL300025277804 none N#CC1=CNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 195, 195, 195, 106, 106, 106, 106, 106, 64, 41, 64, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 195, 106, 106, 106, 106, 106, 106, 41, 41, 1, 106, 106, 106, 201] 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: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277804 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277804
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277804/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277804
Building REAL300025277805
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277805'
/scratch/stefan/7808390/working/building/REAL300025277805 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277805

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277805/0 /scratch/stefan/7808390/working/building/REAL300025277805 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/690
`/scratch/stefan/7808390/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277805 none CC1=CSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 64, 64, 64, 64, 64, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 10, 10, 64, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277805 none CC1=CSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 8, 8, 8, 27, 27, 27, 27, 27, 36, 36, 74, 111, 201, 201, 201, 201, 201, 27, 27, 2, 2, 2, 1, 1, 8, 27, 27, 27, 27, 27, 27, 74, 74, 201, 27, 27, 27] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277805 none CC1=CSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 14, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 118, 118, 118, 64, 64, 64, 64, 64, 47, 37, 47, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 118, 64, 64, 64, 64, 64, 64, 37, 37, 1, 64, 64, 64] 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])
total number of confs: 516
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277805 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277805
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277805/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277805
Building REAL300025277806
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277806'
/scratch/stefan/7808390/working/building/REAL300025277806 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277806

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277806/0 /scratch/stefan/7808390/working/building/REAL300025277806 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/691
`/scratch/stefan/7808390/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277806 none O=C(CCC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 31, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 30, 30, 30, 30, 30, 1, 1, 30, 30, 34, 34, 55, 55, 55, 55, 55, 55, 55, 5, 1, 1, 1, 1, 1, 1, 4, 4, 30, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277806 none O=C(CCC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 6, 4, 1, 1, 1, 1, 1, 24, 24, 55, 55, 55, 55, 55, 63, 63, 85, 130, 201, 201, 201, 201, 201, 55, 55, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 24, 55, 55, 55, 55, 55, 55, 85, 85, 201, 55, 55, 55] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 35, 36, 30, 31] set([0, 1, 2, 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])
total number of confs: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277806 none O=C(CCC1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 143, 137, 201, 201, 201, 30, 30, 30, 30, 30, 25, 21, 25, 10, 1, 1, 1, 1, 1, 1, 1, 30, 30, 143, 143, 151, 151, 201, 201, 201, 201, 201, 201, 201, 68, 30, 30, 30, 30, 30, 30, 21, 21, 1, 30, 30, 30] 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])
total number of confs: 873
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277806 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277806
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277806/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277806
Building REAL300025277807
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277807'
/scratch/stefan/7808390/working/building/REAL300025277807 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277807

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277807/0 /scratch/stefan/7808390/working/building/REAL300025277807 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/692
`/scratch/stefan/7808390/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277807 none CC1=CC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 32, 91, 91, 91, 91, 91, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 18, 18, 91, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277807 none CC1=CC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 5, 5, 5, 20, 20, 20, 20, 20, 49, 49, 115, 151, 201, 201, 201, 201, 201, 20, 20, 1, 2, 2, 2, 1, 2, 2, 2, 5, 20, 20, 20, 20, 20, 20, 115, 115, 201, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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: REAL300025277807 none CC1=CC(C)=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 176, 176, 176, 91, 91, 91, 91, 91, 56, 39, 56, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 176, 91, 91, 91, 91, 91, 91, 39, 39, 1, 91, 91, 91] 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])
total number of confs: 594
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277807 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277807
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277807/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277807
Building REAL300025277808
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277808'
/scratch/stefan/7808390/working/building/REAL300025277808 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277808

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277808/0 /scratch/stefan/7808390/working/building/REAL300025277808 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/693
`/scratch/stefan/7808390/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277808 none O=C(CCC1=NN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 36, 36, 36, 36, 36, 1, 1, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 5, 5, 36, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277808 none O=C(CCC1=NN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 36, 36, 58, 99, 201, 201, 201, 201, 201, 23, 23, 5, 5, 5, 5, 1, 1, 7, 23, 23, 23, 23, 23, 23, 58, 58, 201, 23, 23, 23] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 520
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277808 none O=C(CCC1=NN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [105, 105, 105, 201, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 23, 19, 23, 9, 1, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 201, 201, 105, 36, 36, 36, 36, 36, 36, 19, 19, 1, 36, 36, 36] 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])
total number of confs: 763
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277808 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277808/1 /scratch/stefan/7808390/working/building/REAL300025277808 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/694
`/scratch/stefan/7808390/working/3D/694' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277808.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277808/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277808 none O=C(CCC1=NNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 12, 12, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 30, 30, 30, 30, 30, 1, 1, 12, 12, 12, 12, 22, 22, 6, 1, 1, 1, 1, 1, 1, 5, 5, 30, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277808 none O=C(CCC1=NNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 31, 31, 49, 89, 201, 201, 201, 201, 201, 22, 22, 5, 5, 5, 5, 1, 1, 6, 22, 22, 22, 22, 22, 22, 49, 49, 201, 22, 22, 22] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 472
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277808 none O=C(CCC1=NNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [78, 78, 78, 121, 121, 201, 201, 201, 201, 30, 30, 30, 30, 30, 22, 20, 22, 11, 1, 1, 1, 1, 1, 1, 1, 30, 30, 121, 121, 121, 121, 201, 201, 78, 30, 30, 30, 30, 30, 30, 20, 20, 1, 30, 30, 30] 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])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277808 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277808
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277808/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277808/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277808
Building REAL300025277809
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277809'
/scratch/stefan/7808390/working/building/REAL300025277809 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277809

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277809/0 /scratch/stefan/7808390/working/building/REAL300025277809 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/695
`/scratch/stefan/7808390/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277809 none CC1=CC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 31, 88, 88, 88, 88, 88, 1, 1, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 17, 17, 88, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277809 none CC1=CC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 21, 21, 21, 21, 21, 47, 47, 111, 145, 201, 201, 201, 201, 201, 21, 21, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 21, 21, 21, 111, 111, 201, 21, 21, 21] 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: 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: REAL300025277809 none CC1=CC=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 184, 184, 184, 88, 88, 88, 88, 88, 55, 39, 55, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 184, 88, 88, 88, 88, 88, 88, 39, 39, 1, 88, 88, 88] 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])
total number of confs: 593
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277809 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277809
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277809/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277809
Building REAL300025277810
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277810'
/scratch/stefan/7808390/working/building/REAL300025277810 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277810

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277810/0 /scratch/stefan/7808390/working/building/REAL300025277810 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/696
`/scratch/stefan/7808390/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277810 none CC=C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 142, 201, 142, 142, 80, 80, 80, 80, 80, 53, 43, 53, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 142, 80, 80, 80, 80, 80, 80, 43, 43, 1, 80, 80, 80] 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])
total number of confs: 660
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277810 none CC=C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 16, 80, 80, 80, 80, 80, 1, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 9, 9, 80, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277810 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277810
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277810/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277810
Building REAL300025277811
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277811'
/scratch/stefan/7808390/working/building/REAL300025277811 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277811

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277811/0 /scratch/stefan/7808390/working/building/REAL300025277811 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/697
`/scratch/stefan/7808390/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277811 none O=C(CCC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 33, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 29, 29, 29, 29, 29, 1, 1, 32, 32, 34, 34, 65, 65, 65, 65, 65, 65, 65, 5, 1, 1, 1, 1, 1, 1, 4, 4, 29, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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: REAL300025277811 none O=C(CCC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 7, 5, 1, 1, 1, 1, 1, 1, 30, 30, 65, 65, 65, 65, 65, 68, 68, 92, 137, 201, 201, 201, 201, 201, 65, 65, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 30, 65, 65, 65, 65, 65, 65, 92, 92, 201, 65, 65, 65] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 37, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277811 none O=C(CCC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 162, 164, 201, 201, 201, 201, 29, 29, 29, 29, 29, 23, 20, 23, 11, 1, 1, 1, 1, 1, 1, 1, 29, 29, 162, 162, 166, 166, 201, 201, 201, 201, 201, 201, 201, 68, 29, 29, 29, 29, 29, 29, 20, 20, 1, 29, 29, 29] 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])
total number of confs: 793
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277811 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277811
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277811/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277811
Building REAL300025277812
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277812'
/scratch/stefan/7808390/working/building/REAL300025277812 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277812

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277812/0 /scratch/stefan/7808390/working/building/REAL300025277812 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/698
`/scratch/stefan/7808390/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277812 none O=C(CCC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 12, 1, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 28, 34, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 27, 27, 27, 27, 27, 1, 1, 28, 28, 34, 34, 62, 62, 62, 6, 1, 1, 1, 1, 1, 1, 5, 5, 27, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025277812 none O=C(CCC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 12, 1, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 2, 1, 1, 1, 1, 1, 1, 20, 20, 62, 62, 62, 62, 62, 74, 74, 99, 129, 201, 201, 201, 201, 201, 62, 62, 6, 6, 2, 2, 1, 1, 1, 20, 62, 62, 62, 62, 62, 62, 99, 99, 201, 62, 62, 62] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277812 none O=C(CCC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 12, 1, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [61, 61, 61, 121, 126, 201, 201, 201, 201, 27, 27, 27, 27, 27, 21, 18, 21, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 121, 121, 126, 126, 201, 201, 201, 61, 27, 27, 27, 27, 27, 27, 18, 18, 1, 27, 27, 27] 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])
total number of confs: 641
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277812 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277812
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277812/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277812
Building REAL300025277813
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277813'
/scratch/stefan/7808390/working/building/REAL300025277813 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277813

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277813/0 /scratch/stefan/7808390/working/building/REAL300025277813 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/699
`/scratch/stefan/7808390/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC(F)(F)C3)C2C1)

`REAL300025277813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277813 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC(F)(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 11, 20, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 25, 25, 1, 1, 11, 11, 72, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 25, 25, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 175
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277813 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC(F)(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 32, 13, 1, 1, 1, 1, 1, 1, 1, 53, 72, 72, 72, 72, 72, 109, 109, 109, 201, 201, 201, 201, 201, 72, 72, 32, 32, 1, 72, 72, 72, 72, 72, 72, 109, 201, 201, 201, 201, 201, 72, 72, 72] 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: 638
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: REAL300025277813 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC(F)(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 25, 37, 78, 109, 201, 201, 201, 201, 201, 25, 25, 25, 25, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 78, 78, 201, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 1, 1, 25, 25, 25] 201
rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42, 43])
total number of confs: 524
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277813 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277813
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277813/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277813
Building REAL300025277814
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277814'
/scratch/stefan/7808390/working/building/REAL300025277814 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277814

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277814/0 /scratch/stefan/7808390/working/building/REAL300025277814 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/700
`/scratch/stefan/7808390/working/3D/700' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277814 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 22, 56, 56, 56, 56, 56, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 13, 13, 56, 1, 1, 1, 34, 34] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277814 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 34, 34, 34, 57, 57, 114, 153, 201, 201, 201, 201, 201, 34, 34, 1, 2, 2, 2, 1, 1, 1, 1, 9, 34, 34, 34, 34, 34, 34, 114, 114, 201, 34, 34, 34, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277814 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 83, 83, 83, 56, 56, 56, 56, 56, 41, 35, 41, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 83, 56, 56, 56, 56, 56, 56, 35, 35, 1, 56, 56, 56, 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])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277814 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277814
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277814/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277814
Building REAL300025277815
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277815'
/scratch/stefan/7808390/working/building/REAL300025277815 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277815

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277815/0 /scratch/stefan/7808390/working/building/REAL300025277815 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/701
`/scratch/stefan/7808390/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCCC1)

`REAL300025277815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277815 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 65, 65, 65, 65, 65, 41, 36, 41, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 117, 65, 65, 65, 65, 65, 65, 36, 36, 1, 65, 65, 65, 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])
total number of confs: 626
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277815 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 20, 65, 65, 65, 65, 65, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 15, 15, 65, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277815 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 9, 9, 9, 33, 33, 33, 33, 33, 51, 51, 99, 134, 201, 201, 201, 201, 201, 33, 33, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 33, 33, 33, 99, 99, 201, 33, 33, 33, 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: 571
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277815 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277815
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277815/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277815
Building REAL300025277816
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277816'
/scratch/stefan/7808390/working/building/REAL300025277816 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277816

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277816/0 /scratch/stefan/7808390/working/building/REAL300025277816 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/702
`/scratch/stefan/7808390/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277816 none O=C(CC1CCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 25, 109, 109, 109, 109, 109, 1, 1, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 15, 15, 109, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 272
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277816 none O=C(CC1CCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 29, 29, 29, 29, 29, 44, 44, 84, 114, 201, 201, 201, 201, 201, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 29, 29, 84, 84, 201, 29, 29, 29] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 548
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277816 none O=C(CC1CCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 198, 201, 201, 201, 201, 201, 109, 109, 109, 109, 109, 67, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 109, 109, 109, 109, 109, 109, 31, 31, 1, 109, 109, 109] 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])
total number of confs: 695
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277816 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277816
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277816/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277816
Building REAL300025277817
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277817'
/scratch/stefan/7808390/working/building/REAL300025277817 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277817

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277817/0 /scratch/stefan/7808390/working/building/REAL300025277817 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/703
`/scratch/stefan/7808390/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1)

`REAL300025277817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277817 none CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 51, 51, 51, 51, 51, 1, 1, 30, 30, 30, 30, 30, 30, 24, 24, 6, 1, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1, 1, 30] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277817 none CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in 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, 11, 11, 11, 30, 30, 30, 30, 30, 40, 40, 60, 98, 201, 201, 201, 201, 201, 30, 30, 1, 1, 2, 2, 2, 1, 5, 5, 11, 30, 30, 30, 30, 30, 30, 60, 60, 201, 30, 30, 30, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 46, 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: 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: REAL300025277817 none CC1=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 51, 51, 51, 51, 51, 33, 26, 33, 12, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 123, 51, 51, 51, 51, 51, 51, 26, 26, 1, 51, 51, 51, 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])
total number of confs: 741
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277817 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277817/1 /scratch/stefan/7808390/working/building/REAL300025277817 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/704
`/scratch/stefan/7808390/working/3D/704' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277817.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277817/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277817 none CC1=NNC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 1, 1, 31, 31, 31, 31, 31, 28, 28, 6, 1, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1, 1, 31] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277817 none CC1=NNC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 13, 13, 13, 31, 31, 31, 31, 31, 42, 42, 63, 100, 201, 201, 201, 201, 201, 31, 31, 1, 2, 2, 2, 1, 6, 6, 13, 31, 31, 31, 31, 31, 31, 63, 63, 201, 31, 31, 31, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 520
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277817 none CC1=NNC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 119, 119, 119, 44, 44, 44, 44, 44, 27, 24, 27, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 201, 201, 201, 201, 201, 119, 44, 44, 44, 44, 44, 44, 24, 24, 1, 44, 44, 44, 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])
total number of confs: 761
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277817 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277817
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277817/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277817/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277817
Building REAL300025277818
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277818'
/scratch/stefan/7808390/working/building/REAL300025277818 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277818

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277818/0 /scratch/stefan/7808390/working/building/REAL300025277818 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/705
`/scratch/stefan/7808390/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277818 none O=C(C=C1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 18, 55, 55, 55, 55, 55, 1, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 14, 14, 55, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277818 none O=C(C=C1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 29, 29, 50, 50, 106, 136, 201, 201, 201, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 29, 106, 106, 201, 29, 29, 29] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277818 none O=C(C=C1CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [123, 123, 123, 201, 201, 201, 201, 55, 55, 55, 55, 55, 35, 31, 35, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 201, 123, 55, 55, 55, 55, 55, 55, 31, 31, 1, 55, 55, 55] 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])
total number of confs: 632
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277818 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277818
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277818/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277818
Building REAL300025277819
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277819'
/scratch/stefan/7808390/working/building/REAL300025277819 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277819

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277819/0 /scratch/stefan/7808390/working/building/REAL300025277819 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/706
`/scratch/stefan/7808390/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC(F)=C3)C2C1)

`REAL300025277819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277819 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens 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, 12, 20, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 19, 1, 1, 12, 12, 58, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277819 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 40, 58, 58, 58, 58, 58, 86, 86, 86, 201, 201, 201, 201, 201, 201, 58, 58, 31, 31, 1, 58, 58, 58, 58, 58, 58, 86, 201, 201, 201, 58, 58, 58] 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: 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: REAL300025277819 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CC(F)=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens 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, 19, 37, 70, 105, 201, 201, 201, 201, 201, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 70, 70, 201, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 19, 19, 19] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 496
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277819 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277819
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277819/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277819
Building REAL300025277820
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277820'
/scratch/stefan/7808390/working/building/REAL300025277820 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277820

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277820/0 /scratch/stefan/7808390/working/building/REAL300025277820 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/707
`/scratch/stefan/7808390/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)CC)

`REAL300025277820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277820 none CCC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 105, 105, 75, 75, 75, 46, 46, 46, 46, 46, 33, 27, 33, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 105, 171, 171, 171, 171, 171, 171, 105, 75, 46, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 46, 171, 171, 171, 171, 171] 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: 1144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277820 none CCC(=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 1, 14, 22, 22, 22, 22, 22, 22, 14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1, 1, 22, 22, 22, 22, 22] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277820 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277820
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277820/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277820
Building REAL300025277821
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277821'
/scratch/stefan/7808390/working/building/REAL300025277821 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277821

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277821/0 /scratch/stefan/7808390/working/building/REAL300025277821 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/708
`/scratch/stefan/7808390/working/3D/708' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NC=C3)C2C1)

`REAL300025277821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277821 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 10, 17, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 19, 1, 1, 10, 10, 54, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277821 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 37, 54, 54, 54, 54, 54, 88, 88, 88, 201, 201, 201, 201, 201, 201, 54, 54, 32, 32, 1, 54, 54, 54, 54, 54, 54, 88, 201, 201, 201, 201, 54, 54, 54] 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: 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: REAL300025277821 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 19, 33, 67, 110, 201, 201, 201, 201, 201, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 67, 67, 201, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 19, 19, 19] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 509
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277821 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277821
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277821/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277821
Building REAL300025277822
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277822'
/scratch/stefan/7808390/working/building/REAL300025277822 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277822

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277822/0 /scratch/stefan/7808390/working/building/REAL300025277822 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/709
`/scratch/stefan/7808390/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277822 none CC(C)=C(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 1, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 137, 201, 137, 137, 56, 56, 56, 56, 56, 39, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 137, 56, 56, 56, 56, 56, 56, 33, 33, 1, 56, 56, 56] 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])
total number of confs: 660
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277822 none CC(C)=C(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 1, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [23, 23, 23, 6, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 56, 56, 56, 56, 56, 1, 1, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 9, 9, 56, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277822 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277822
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277822/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277822
Building REAL300025277823
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277823'
/scratch/stefan/7808390/working/building/REAL300025277823 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277823

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277823/0 /scratch/stefan/7808390/working/building/REAL300025277823 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/710
`/scratch/stefan/7808390/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC(=O)C3)C2C1)

`REAL300025277823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277823 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC(=O)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 10, 17, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 1, 1, 10, 10, 58, 1, 1, 1, 1, 1, 1, 4, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1] 127
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 143
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: REAL300025277823 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC(=O)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [46, 28, 13, 1, 1, 1, 1, 1, 1, 1, 46, 58, 58, 58, 58, 58, 79, 79, 79, 127, 127, 127, 127, 127, 127, 58, 58, 28, 28, 1, 58, 58, 58, 58, 58, 58, 79, 127, 127, 127, 127, 127, 127, 127, 127, 58, 58, 58] 127
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: 423
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277823 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC(=O)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [26, 19, 26, 50, 77, 127, 127, 127, 127, 127, 19, 19, 19, 19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 127, 19, 19, 19, 19, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19] 127
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47])
total number of confs: 332
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277823 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277823
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277823/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277823
Building REAL300025277824
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277824'
/scratch/stefan/7808390/working/building/REAL300025277824 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277824

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277824/0 /scratch/stefan/7808390/working/building/REAL300025277824 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/711
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CCCC3)C2C1)

`REAL300025277824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277824 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 15, 31, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 1, 1, 15, 15, 133, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 23, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277824 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 52, 13, 1, 1, 1, 1, 1, 1, 1, 88, 133, 133, 133, 133, 133, 200, 200, 200, 201, 201, 201, 201, 133, 133, 52, 52, 1, 133, 133, 133, 133, 133, 133, 200, 201, 201, 201, 201, 201, 201, 201, 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, 44])
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: REAL300025277824 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 26, 41, 84, 122, 201, 201, 201, 201, 201, 26, 26, 26, 26, 11, 11, 1, 11, 1, 1, 1, 1, 1, 26, 26, 84, 84, 201, 26, 26, 26, 26, 26, 26, 11, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44])
total number of confs: 506
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277824 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277824
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277824/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277824
Building REAL300025277825
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277825'
/scratch/stefan/7808390/working/building/REAL300025277825 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277825

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277825/0 /scratch/stefan/7808390/working/building/REAL300025277825 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/712
`/scratch/stefan/7808390/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(F)=C3CCCC3)C2C1)

`REAL300025277825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277825 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(F)=C3CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 16, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 25, 25, 25, 25, 25, 1, 1, 9, 9, 84, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277825 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(F)=C3CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 47, 13, 1, 1, 1, 1, 1, 1, 1, 56, 84, 84, 84, 84, 84, 181, 181, 181, 201, 201, 201, 201, 201, 201, 84, 84, 47, 47, 1, 84, 84, 84, 84, 84, 84, 181, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84] 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: 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: REAL300025277825 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(F)=C3CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 25, 35, 69, 103, 201, 201, 201, 201, 201, 25, 25, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 25, 25, 69, 69, 201, 25, 25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47])
total number of confs: 494
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277825 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277825
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277825/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277825
Building REAL300025277826
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277826'
/scratch/stefan/7808390/working/building/REAL300025277826 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277826

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277826/0 /scratch/stefan/7808390/working/building/REAL300025277826 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/713
`/scratch/stefan/7808390/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277826 none CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 16, 59, 59, 59, 59, 59, 1, 1, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 8, 8, 59, 1, 1, 1, 19] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277826 none CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 19, 19, 19, 19, 19, 31, 31, 68, 111, 201, 201, 201, 201, 201, 19, 19, 1, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 19, 19, 68, 68, 201, 19, 19, 19, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 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])
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: REAL300025277826 none CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 123, 123, 123, 59, 59, 59, 59, 59, 40, 34, 40, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 123, 59, 59, 59, 59, 59, 59, 34, 34, 1, 59, 59, 59, 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])
total number of confs: 526
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277826 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277826
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277826/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277826
Building REAL300025277827
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277827'
/scratch/stefan/7808390/working/building/REAL300025277827 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277827

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277827/0 /scratch/stefan/7808390/working/building/REAL300025277827 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/714
`/scratch/stefan/7808390/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277827 none CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 50, 129, 129, 129, 129, 129, 1, 1, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 29, 29, 129, 1, 1, 1, 10] 174
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 269
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277827 none CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 26, 26, 76, 112, 174, 174, 174, 174, 174, 10, 10, 1, 2, 2, 2, 1, 4, 10, 10, 10, 10, 10, 10, 76, 76, 174, 10, 10, 10, 1] 174
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: 460
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277827 none CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 174, 174, 174, 174, 174, 174, 129, 129, 129, 129, 129, 79, 42, 79, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 174, 174, 174, 174, 174, 174, 129, 129, 129, 129, 129, 129, 42, 42, 1, 129, 129, 129, 174] 174
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: 520
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277827 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277827
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277827/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277827
Building REAL300025277828
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277828'
/scratch/stefan/7808390/working/building/REAL300025277828 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277828

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277828/0 /scratch/stefan/7808390/working/building/REAL300025277828 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/715
`/scratch/stefan/7808390/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1COC(=O)C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277828 none O=C(CC1COC(=O)C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 11, 5, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 28, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 56, 56, 56, 56, 56, 1, 1, 28, 28, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 1, 1, 5, 5, 56, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277828 none O=C(CC1COC(=O)C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 11, 5, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [19, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 42, 42, 42, 42, 42, 58, 58, 81, 123, 201, 201, 201, 201, 201, 42, 42, 6, 6, 1, 1, 1, 1, 1, 19, 42, 42, 42, 42, 42, 42, 81, 81, 201, 42, 42, 42] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 546
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277828 none O=C(CC1COC(=O)C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 11, 5, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [112, 112, 112, 196, 201, 201, 201, 201, 201, 56, 56, 56, 56, 56, 34, 28, 34, 12, 1, 1, 1, 1, 1, 1, 1, 56, 56, 196, 196, 201, 201, 201, 201, 201, 112, 56, 56, 56, 56, 56, 56, 28, 28, 1, 56, 56, 56] 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])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277828 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277828
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277828/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277828
Building REAL300025277829
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277829'
/scratch/stefan/7808390/working/building/REAL300025277829 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277829

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277829/0 /scratch/stefan/7808390/working/building/REAL300025277829 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/716
`/scratch/stefan/7808390/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277829 none CC1=C(C)OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 5, 12, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 46, 119, 119, 119, 119, 119, 1, 1, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 26, 26, 119, 1, 1, 1, 17] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 256
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277829 none CC1=C(C)OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 5, 12, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 17, 17, 17, 17, 17, 38, 38, 107, 145, 201, 201, 201, 201, 201, 17, 17, 1, 2, 2, 2, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 107, 107, 201, 17, 17, 17, 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: 555
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277829 none CC1=C(C)OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 5, 12, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 119, 119, 119, 119, 119, 78, 44, 78, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 201, 201, 200, 119, 119, 119, 119, 119, 119, 44, 44, 1, 119, 119, 119, 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])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277829 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277829
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277829/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277829
Building REAL300025277830
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277830'
/scratch/stefan/7808390/working/building/REAL300025277830 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277830

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277830/0 /scratch/stefan/7808390/working/building/REAL300025277830 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/717
`/scratch/stefan/7808390/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277830 none O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 20, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 34, 34, 34, 34, 34, 1, 1, 20, 20, 47, 47, 47, 47, 6, 1, 1, 1, 1, 1, 1, 8, 8, 34, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277830 none O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 1, 1, 1, 1, 1, 1, 1, 13, 13, 47, 47, 47, 47, 47, 72, 72, 102, 154, 201, 201, 201, 201, 201, 47, 47, 7, 7, 1, 1, 1, 1, 13, 47, 47, 47, 47, 47, 47, 102, 102, 201, 47, 47, 47] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277830 none O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [61, 61, 61, 135, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 24, 24, 24, 11, 1, 1, 1, 1, 1, 1, 1, 34, 34, 135, 135, 201, 201, 201, 201, 61, 34, 34, 34, 34, 34, 34, 24, 24, 1, 34, 34, 34] 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])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277830 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277830
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277830/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277830
Building REAL300025277831
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277831'
/scratch/stefan/7808390/working/building/REAL300025277831 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277831

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277831/0 /scratch/stefan/7808390/working/building/REAL300025277831 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/718
`/scratch/stefan/7808390/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCO3)C2C1)

`REAL300025277831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277831 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 19, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 1, 1, 9, 9, 89, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277831 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 13, 1, 1, 1, 1, 1, 1, 1, 57, 89, 89, 89, 89, 89, 182, 182, 182, 201, 201, 201, 201, 201, 89, 89, 44, 44, 1, 89, 89, 89, 89, 89, 89, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89] 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: 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: REAL300025277831 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 37, 78, 122, 201, 201, 201, 201, 201, 24, 24, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 78, 78, 201, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 35, 45, 46, 47])
total number of confs: 528
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277831 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277831
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277831/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277831
Building REAL300025277832
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277832'
/scratch/stefan/7808390/working/building/REAL300025277832 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277832

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277832/0 /scratch/stefan/7808390/working/building/REAL300025277832 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/719
`/scratch/stefan/7808390/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1=O)

`REAL300025277832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277832 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1=O 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 4, 1, 1, 1] 6
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277832 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1=O 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 5] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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])
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: REAL300025277832 none CC1=NNC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1=O 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
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, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4] 6
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])
total number of confs: 13
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277832 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277832
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277832/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277832
Building REAL300025277833
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277833'
/scratch/stefan/7808390/working/building/REAL300025277833 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277833

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277833/0 /scratch/stefan/7808390/working/building/REAL300025277833 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/720
`/scratch/stefan/7808390/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(SC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277833 none CCC(SC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 188, 151, 188, 201, 151, 151, 71, 71, 71, 71, 71, 41, 34, 41, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 195, 195, 195, 195, 195, 188, 201, 201, 201, 151, 71, 71, 71, 71, 71, 71, 34, 34, 1, 71, 71, 71] 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])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277833 none CCC(SC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 14, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 16, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 71, 71, 71, 71, 71, 1, 1, 21, 21, 21, 21, 21, 16, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 6, 6, 71, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277833 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277833
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277833/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277833
Building REAL300025277834
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277834'
/scratch/stefan/7808390/working/building/REAL300025277834 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277834

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277834/0 /scratch/stefan/7808390/working/building/REAL300025277834 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/721
`/scratch/stefan/7808390/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NC=N1)

`REAL300025277834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277834 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NC=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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 118, 118, 118, 118, 118, 1, 1, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 26, 26, 118, 1, 1, 1, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277834 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NC=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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 15, 15, 15, 15, 15, 35, 35, 104, 149, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 2, 2, 2, 1, 4, 15, 15, 15, 15, 15, 15, 104, 104, 201, 15, 15, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25, 26, 30] set([5, 6, 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])
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: REAL300025277834 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NC=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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 118, 118, 118, 118, 118, 75, 43, 75, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 200, 118, 118, 118, 118, 118, 118, 43, 43, 1, 118, 118, 118, 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])
total number of confs: 635
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277834 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277834
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277834/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277834
Building REAL300025277835
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277835'
/scratch/stefan/7808390/working/building/REAL300025277835 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277835

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277835/0 /scratch/stefan/7808390/working/building/REAL300025277835 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/722
`/scratch/stefan/7808390/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277835 none CC1(C)CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 25, 82, 82, 82, 82, 82, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 14, 14, 82, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 178
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277835 none CC1(C)CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 17, 17, 17, 17, 17, 33, 33, 74, 115, 201, 201, 201, 201, 201, 17, 17, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 74, 74, 201, 17, 17, 17] 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])
total number of confs: 510
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277835 none CC1(C)CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 155, 155, 155, 82, 82, 82, 82, 82, 59, 34, 59, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 82, 82, 82, 82, 82, 82, 34, 34, 1, 82, 82, 82] 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])
total number of confs: 660
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277835 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277835
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277835/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277835
Building REAL300025277836
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277836'
/scratch/stefan/7808390/working/building/REAL300025277836 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277836

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277836/0 /scratch/stefan/7808390/working/building/REAL300025277836 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/723
`/scratch/stefan/7808390/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)OCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277836 none CCC(C)OCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 141, 141, 141, 65, 65, 65, 65, 65, 42, 35, 42, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 141, 65, 65, 65, 65, 65, 65, 35, 35, 1, 65, 65, 65] 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])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277836 none CCC(C)OCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 41, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 65, 65, 65, 65, 65, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 18, 18, 6, 1, 1, 1, 1, 1, 1, 6, 6, 65, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 206
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277836 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277836
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277836/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277836
Building REAL300025277837
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277837'
/scratch/stefan/7808390/working/building/REAL300025277837 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277837

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277837/0 /scratch/stefan/7808390/working/building/REAL300025277837 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/724
`/scratch/stefan/7808390/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277837 none CC1(C)C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 15, 55, 55, 55, 55, 55, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 9, 9, 55, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277837 none CC1(C)C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 20, 20, 20, 20, 20, 32, 32, 67, 108, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 20, 20, 67, 67, 201, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5] 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: 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: REAL300025277837 none CC1(C)C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 135, 201, 135, 135, 55, 55, 55, 55, 55, 41, 34, 41, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 135, 55, 55, 55, 55, 55, 55, 34, 34, 1, 55, 55, 55] 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])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277837 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277837
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277837/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277837
Building REAL300025277838
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277838'
/scratch/stefan/7808390/working/building/REAL300025277838 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277838

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277838/0 /scratch/stefan/7808390/working/building/REAL300025277838 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/725
`/scratch/stefan/7808390/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277838 none CC(O)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [199, 186, 201, 102, 102, 102, 43, 43, 43, 43, 43, 31, 29, 31, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 199, 201, 201, 201, 201, 201, 603, 186, 186, 102, 43, 43, 43, 43, 43, 43, 29, 29, 1, 43, 43, 43, 201, 201, 201, 201, 201] 603
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: 1412
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: REAL300025277838 none CC(O)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [32, 27, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 43, 43, 43, 43, 43, 1, 1, 31, 37, 37, 35, 35, 35, 105, 27, 27, 6, 1, 1, 1, 1, 1, 1, 6, 6, 43, 1, 1, 1, 37, 37, 37, 37, 37] 603
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50])
total number of confs: 359
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: REAL300025277838 none CC(O)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 6, 11, 11, 11, 37, 37, 37, 37, 37, 45, 45, 68, 94, 201, 201, 201, 201, 201, 37, 37, 1, 1, 1, 3, 3, 3, 9, 6, 6, 11, 37, 37, 37, 37, 37, 37, 68, 68, 201, 37, 37, 37, 1, 1, 1, 1, 1] 603
rigid atoms, others: [1, 46, 47, 48, 49, 50, 24, 25, 26] set([0, 2, 3, 4, 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])
total number of confs: 505
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277838 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277838
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277838/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277838
Building REAL300025277839
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277839'
/scratch/stefan/7808390/working/building/REAL300025277839 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277839

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277839/0 /scratch/stefan/7808390/working/building/REAL300025277839 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/726
`/scratch/stefan/7808390/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277839 none CSC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 177, 192, 101, 101, 101, 47, 47, 47, 47, 47, 34, 31, 34, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 192, 192, 192, 192, 177, 177, 101, 47, 47, 47, 47, 47, 47, 31, 31, 1, 47, 47, 47] 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])
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: REAL300025277839 none CSC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 25, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 47, 47, 47, 47, 47, 1, 1, 47, 47, 47, 33, 33, 33, 33, 25, 25, 6, 1, 1, 1, 1, 1, 1, 5, 5, 47, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277839 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277839
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277839/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277839
Building REAL300025277840
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277840'
/scratch/stefan/7808390/working/building/REAL300025277840 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277840

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277840/0 /scratch/stefan/7808390/working/building/REAL300025277840 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/727
`/scratch/stefan/7808390/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277840 none O=C(CN1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 12, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 67, 67, 67, 67, 67, 1, 1, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 6, 6, 67, 1, 1, 1] 201
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 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: REAL300025277840 none O=C(CN1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 12, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 9, 9, 25, 25, 25, 25, 25, 36, 36, 62, 106, 201, 201, 201, 201, 201, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 62, 62, 201, 25, 25, 25] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 520
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277840 none O=C(CN1CCOCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 12, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 40, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 67, 67, 67, 67, 67, 67, 29, 29, 1, 67, 67, 67] 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])
total number of confs: 738
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277840 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277840
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277840/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277840
Building REAL300025277841
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277841'
/scratch/stefan/7808390/working/building/REAL300025277841 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277841

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277841/0 /scratch/stefan/7808390/working/building/REAL300025277841 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/728
`/scratch/stefan/7808390/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCCO3)C2C1)

`REAL300025277841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277841 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 10, 20, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 1, 1, 10, 10, 88, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 21, 21, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277841 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 13, 1, 1, 1, 1, 1, 1, 1, 57, 88, 88, 88, 88, 88, 186, 186, 186, 201, 201, 201, 201, 201, 88, 88, 44, 44, 1, 88, 88, 88, 88, 88, 88, 186, 201, 201, 201, 201, 201, 201, 88, 88, 88] 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])
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: REAL300025277841 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 74, 117, 201, 201, 201, 201, 201, 21, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 74, 74, 201, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 35, 42, 43, 44])
total number of confs: 520
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277841 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277841
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277841/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277841
Building REAL300025277842
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277842'
/scratch/stefan/7808390/working/building/REAL300025277842 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277842

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277842/0 /scratch/stefan/7808390/working/building/REAL300025277842 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/729
`/scratch/stefan/7808390/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=NC=N1)

`REAL300025277842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277842 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 138, 138, 138, 85, 85, 85, 85, 85, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 85, 85, 85, 85, 85, 85, 30, 30, 1, 85, 85, 85, 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])
total number of confs: 748
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277842 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 85, 85, 85, 85, 85, 1, 1, 17, 29, 29, 29, 29, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 10, 10, 85, 1, 1, 1, 29, 29] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 43, 20, 21, 41, 36, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277842 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)N1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 19, 19, 19, 29, 29, 29, 29, 29, 40, 40, 72, 109, 201, 201, 201, 201, 201, 29, 29, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 29, 29, 29, 29, 29, 29, 72, 72, 201, 29, 29, 29, 1, 1] 201
rigid atoms, others: [1, 44, 45, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/7808390/working/building/REAL300025277842 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277842
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277842/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277842
Building REAL300025277843
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277843'
/scratch/stefan/7808390/working/building/REAL300025277843 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277843

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277843/0 /scratch/stefan/7808390/working/building/REAL300025277843 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/730
`/scratch/stefan/7808390/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCOCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277843 none CN1CCOCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 12, 12, 12, 12, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1] 14
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277843 none CN1CCOCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 8, 11, 14, 14, 14, 14, 14, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 8, 8, 14, 5, 5, 5] 14
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 36, 5, 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])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277843 none CN1CCOCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12, 12] 14
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])
total number of confs: 41
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277843 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277843
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277843/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277843
Building REAL300025277844
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277844'
/scratch/stefan/7808390/working/building/REAL300025277844 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277844

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277844/0 /scratch/stefan/7808390/working/building/REAL300025277844 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/731
`/scratch/stefan/7808390/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277844 none CC1=NSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [25, 19, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 60, 60, 60, 60, 60, 1, 1, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 9, 9, 60, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277844 none CC1=NSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 8, 8, 8, 25, 25, 25, 25, 25, 38, 38, 74, 103, 201, 201, 201, 201, 201, 25, 25, 2, 2, 2, 1, 8, 25, 25, 25, 25, 25, 25, 74, 74, 201, 25, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 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: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277844 none CC1=NSC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 119, 119, 119, 60, 60, 60, 60, 60, 42, 35, 42, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 119, 60, 60, 60, 60, 60, 60, 35, 35, 1, 60, 60, 60] 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])
total number of confs: 508
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277844 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277844
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277844/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277844
Building REAL300025277845
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277845'
/scratch/stefan/7808390/working/building/REAL300025277845 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277845

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277845/0 /scratch/stefan/7808390/working/building/REAL300025277845 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/732
`/scratch/stefan/7808390/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277845 none C#CCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 196, 189, 189, 68, 68, 68, 31, 31, 31, 31, 31, 26, 23, 26, 13, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 196, 196, 196, 196, 189, 189, 68, 31, 31, 31, 31, 31, 31, 23, 23, 1, 31, 31, 31] 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])
total number of confs: 793
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277845 none C#CCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 39, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 31, 31, 31, 31, 31, 1, 1, 59, 59, 59, 43, 43, 43, 43, 35, 35, 5, 1, 1, 1, 1, 1, 1, 4, 4, 31, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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
/scratch/stefan/7808390/working/building/REAL300025277845 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277845
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277845/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277845
Building REAL300025277846
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277846'
/scratch/stefan/7808390/working/building/REAL300025277846 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277846

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277846/0 /scratch/stefan/7808390/working/building/REAL300025277846 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/733
`/scratch/stefan/7808390/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCNC(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277846 none C#CCNC(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 190, 201, 81, 81, 81, 35, 35, 35, 35, 35, 25, 22, 25, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 190, 190, 81, 35, 35, 35, 35, 35, 35, 22, 22, 1, 35, 35, 35] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277846 none C#CCNC(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [45, 45, 36, 36, 25, 36, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 35, 35, 35, 35, 35, 1, 1, 45, 45, 45, 36, 25, 25, 5, 1, 1, 1, 1, 1, 1, 5, 5, 35, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277846 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277846
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277846/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277846
Building REAL300025277847
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277847'
/scratch/stefan/7808390/working/building/REAL300025277847 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277847

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277847/0 /scratch/stefan/7808390/working/building/REAL300025277847 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/734
`/scratch/stefan/7808390/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277847 none CCNC(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 140, 152, 84, 84, 84, 33, 33, 33, 33, 33, 24, 22, 24, 10, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 152, 140, 140, 84, 33, 33, 33, 33, 33, 33, 22, 22, 1, 33, 33, 33] 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])
total number of confs: 874
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277847 none CCNC(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 27, 27, 17, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 33, 33, 33, 33, 33, 1, 1, 44, 44, 44, 44, 44, 27, 17, 17, 5, 1, 1, 1, 1, 1, 1, 5, 5, 33, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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
/scratch/stefan/7808390/working/building/REAL300025277847 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277847
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277847/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277847
Building REAL300025277848
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277848'
/scratch/stefan/7808390/working/building/REAL300025277848 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277848

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277848/0 /scratch/stefan/7808390/working/building/REAL300025277848 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/735
`/scratch/stefan/7808390/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277848 none CNC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 170, 75, 75, 75, 38, 38, 38, 38, 38, 24, 20, 24, 11, 1, 1, 1, 1, 1, 1, 1, 38, 38, 201, 201, 201, 201, 189, 187, 183, 183, 170, 170, 75, 38, 38, 38, 38, 38, 38, 20, 20, 1, 38, 38, 38] 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])
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: REAL300025277848 none CNC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 34, 22, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 1, 1, 34, 34, 34, 34, 31, 30, 28, 28, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1, 1] 201
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277848 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277848
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277848/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277848
Building REAL300025277849
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277849'
/scratch/stefan/7808390/working/building/REAL300025277849 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277849

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277849/0 /scratch/stefan/7808390/working/building/REAL300025277849 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/736
`/scratch/stefan/7808390/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277849 none COC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 16, 16, 16, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 40, 109, 109, 109, 109, 109, 1, 1, 16, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 24, 24, 109, 1, 1, 1, 16] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39, 43])
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: REAL300025277849 none COC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 5, 5, 5, 16, 16, 16, 16, 16, 39, 39, 90, 128, 201, 201, 201, 201, 201, 16, 16, 1, 2, 2, 2, 5, 16, 16, 16, 16, 16, 16, 90, 90, 201, 16, 16, 16, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 26] set([0, 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])
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: REAL300025277849 none COC1=NOC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 198, 198, 198, 109, 109, 109, 109, 109, 65, 41, 65, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 198, 109, 109, 109, 109, 109, 109, 41, 41, 1, 109, 109, 109, 201] 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: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277849 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277849
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277849/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277849
Building REAL300025277850
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277850'
/scratch/stefan/7808390/working/building/REAL300025277850 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277850

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277850/0 /scratch/stefan/7808390/working/building/REAL300025277850 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/737
`/scratch/stefan/7808390/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277850 none COC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 196, 106, 106, 106, 48, 48, 48, 48, 48, 30, 24, 30, 12, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 106, 48, 48, 48, 48, 48, 48, 24, 24, 1, 48, 48, 48] 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])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277850 none COC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 48, 48, 48, 48, 48, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 26, 26, 6, 1, 1, 1, 1, 1, 1, 5, 5, 48, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277850 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277850
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277850/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277850
Building REAL300025277851
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277851'
/scratch/stefan/7808390/working/building/REAL300025277851 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277851

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277851/0 /scratch/stefan/7808390/working/building/REAL300025277851 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/738
`/scratch/stefan/7808390/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1)

`REAL300025277851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277851 none CCC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [32, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 83, 83, 83, 83, 83, 1, 1, 9, 9, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 7, 7, 83, 1, 1, 1, 9] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
total number of confs: 228
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277851 none CCC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [7, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 15, 15, 33, 59, 169, 169, 169, 169, 169, 9, 9, 1, 1, 7, 7, 7, 7, 7, 4, 9, 9, 9, 9, 9, 9, 33, 33, 169, 9, 9, 9, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 45, 25, 26] set([0, 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])
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: REAL300025277851 none CCC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 169, 169, 169, 168, 168, 168, 83, 83, 83, 83, 83, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 169, 169, 201, 201, 201, 201, 201, 168, 83, 83, 83, 83, 83, 83, 31, 31, 1, 83, 83, 83, 169] 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: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277851 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277851
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277851/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277851
Building REAL300025277852
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277852'
/scratch/stefan/7808390/working/building/REAL300025277852 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277852

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277852/0 /scratch/stefan/7808390/working/building/REAL300025277852 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/739
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1)

`REAL300025277852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277852 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 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, 7, 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: [6, 1, 6, 18, 34, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 1, 1, 18, 18, 125, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
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: REAL300025277852 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 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, 7, 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: [79, 48, 13, 1, 1, 1, 1, 1, 1, 1, 79, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 48, 48, 1, 125, 125, 125, 125, 125, 125, 201, 201, 201, 201, 125, 125, 125] 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: 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: REAL300025277852 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 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, 7, 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: [23, 10, 23, 69, 117, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 69, 201, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277852 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277852
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277852/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277852
Building REAL300025277853
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277853'
/scratch/stefan/7808390/working/building/REAL300025277853 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277853

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277853/0 /scratch/stefan/7808390/working/building/REAL300025277853 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/740
`/scratch/stefan/7808390/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1N)

`REAL300025277853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277853 none CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1N 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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 27, 69, 69, 69, 69, 69, 1, 1, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 16, 16, 69, 1, 1, 1, 30, 30] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45])
total number of confs: 173
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: REAL300025277853 none CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1N 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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 30, 30, 30, 30, 30, 54, 54, 111, 148, 201, 201, 201, 201, 201, 30, 30, 1, 1, 2, 2, 2, 1, 8, 30, 30, 30, 30, 30, 30, 111, 111, 201, 30, 30, 30, 2, 2] 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: 619
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: REAL300025277853 none CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1N 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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 146, 146, 146, 69, 69, 69, 69, 69, 45, 34, 45, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 146, 69, 69, 69, 69, 69, 69, 34, 34, 1, 69, 69, 69, 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])
total number of confs: 523
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277853 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277853
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277853/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277853
Building REAL300025277854
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277854'
/scratch/stefan/7808390/working/building/REAL300025277854 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277854

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277854/0 /scratch/stefan/7808390/working/building/REAL300025277854 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/741
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CN=CN=C3)C2C1)

`REAL300025277854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277854 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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, 1, 6, 15, 31, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 8, 10, 10, 1, 1, 15, 15, 98, 1, 1, 1, 1, 1, 1, 6, 10, 9, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277854 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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: [63, 41, 13, 1, 1, 1, 1, 1, 1, 1, 63, 98, 98, 98, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 41, 41, 1, 98, 98, 98, 98, 98, 98, 201, 201, 201, 201, 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])
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: REAL300025277854 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 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: [30, 11, 30, 70, 123, 201, 201, 201, 201, 201, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 70, 70, 201, 11, 11, 11, 11, 11, 11, 3, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [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, 34, 35, 39, 40, 41])
total number of confs: 482
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277854 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277854
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277854/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277854
Building REAL300025277855
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277855'
/scratch/stefan/7808390/working/building/REAL300025277855 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277855

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277855/0 /scratch/stefan/7808390/working/building/REAL300025277855 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/742
`/scratch/stefan/7808390/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCOCC3)C2C1)

`REAL300025277855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277855 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 11, 22, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 1, 1, 11, 11, 78, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1] 139
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 45, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277855 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [60, 36, 13, 1, 1, 1, 1, 1, 1, 1, 60, 78, 78, 78, 78, 78, 118, 118, 118, 139, 139, 139, 139, 139, 78, 78, 36, 36, 1, 78, 78, 78, 78, 78, 78, 118, 139, 139, 139, 139, 139, 139, 139, 78, 78, 78] 139
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: 415
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277855 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [27, 17, 27, 55, 84, 139, 139, 139, 139, 139, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 55, 55, 139, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 139
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 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, 35, 43, 44, 45])
total number of confs: 365
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277855 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277855
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277855/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277855
Building REAL300025277856
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277856'
/scratch/stefan/7808390/working/building/REAL300025277856 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277856

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277856/0 /scratch/stefan/7808390/working/building/REAL300025277856 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/743
`/scratch/stefan/7808390/working/3D/743' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277856 none O=C(CC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 12, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 21, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 13, 39, 39, 39, 39, 39, 1, 1, 21, 21, 41, 41, 41, 6, 1, 1, 1, 1, 1, 1, 9, 9, 39, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 189
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277856 none O=C(CC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 12, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 65, 65, 104, 148, 201, 201, 201, 201, 201, 41, 41, 2, 2, 1, 1, 1, 9, 41, 41, 41, 41, 41, 41, 104, 104, 201, 41, 41, 41] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025277856 none O=C(CC1=COC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 12, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [68, 68, 68, 124, 201, 201, 201, 201, 39, 39, 39, 39, 39, 25, 25, 25, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 124, 124, 201, 201, 201, 68, 39, 39, 39, 39, 39, 39, 25, 25, 1, 39, 39, 39] 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])
total number of confs: 608
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277856 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277856
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277856/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277856
Building REAL300025277857
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277857'
/scratch/stefan/7808390/working/building/REAL300025277857 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277857

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277857/0 /scratch/stefan/7808390/working/building/REAL300025277857 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/744
`/scratch/stefan/7808390/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1)

`REAL300025277857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277857 none CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 46, 122, 122, 122, 122, 122, 1, 1, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 26, 26, 122, 1, 1, 1, 12] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42])
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: REAL300025277857 none CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 3, 3, 12, 12, 12, 12, 12, 35, 35, 102, 145, 201, 201, 201, 201, 201, 12, 12, 1, 1, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 102, 102, 201, 12, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 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])
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: REAL300025277857 none CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 122, 122, 122, 122, 122, 77, 41, 77, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 122, 41, 41, 1, 122, 122, 122, 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])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277857 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277857
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277857/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277857
Building REAL300025277858
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277858'
/scratch/stefan/7808390/working/building/REAL300025277858 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277858

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277858/0 /scratch/stefan/7808390/working/building/REAL300025277858 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/745
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CCCCCC3)C2C1)

`REAL300025277858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277858 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 13, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 29, 1, 1, 8, 8, 46, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 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: REAL300025277858 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 13, 1, 1, 1, 1, 1, 1, 1, 33, 46, 46, 46, 46, 46, 109, 109, 109, 201, 201, 201, 201, 201, 201, 46, 46, 28, 28, 1, 46, 46, 46, 46, 46, 46, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 46, 46] 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: 461
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: REAL300025277858 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CCCCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 73, 108, 201, 201, 201, 201, 201, 29, 29, 29, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29, 73, 73, 201, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 504
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277858 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277858
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277858/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277858
Building REAL300025277859
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277859'
/scratch/stefan/7808390/working/building/REAL300025277859 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277859

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277859/0 /scratch/stefan/7808390/working/building/REAL300025277859 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/746
`/scratch/stefan/7808390/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](NC(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277859 none C[C@H](NC(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 129, 201, 201, 201, 201, 201, 129, 129, 53, 53, 53, 53, 53, 33, 26, 33, 11, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 201, 129, 53, 53, 53, 53, 53, 53, 26, 26, 1, 53, 53, 53] 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])
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: REAL300025277859 none C[C@H](NC(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [29, 6, 29, 29, 35, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 53, 53, 53, 53, 53, 1, 1, 29, 29, 29, 35, 35, 35, 6, 1, 1, 1, 1, 1, 1, 5, 5, 53, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277859 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277859
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277859/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277859
Building REAL300025277860
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277860'
/scratch/stefan/7808390/working/building/REAL300025277860 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277860

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277860/0 /scratch/stefan/7808390/working/building/REAL300025277860 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/747
`/scratch/stefan/7808390/working/3D/747' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1OCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277860 none O=C(CC1OCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 54, 54, 54, 54, 54, 1, 1, 35, 35, 49, 49, 49, 49, 49, 49, 49, 6, 1, 1, 1, 1, 1, 1, 5, 5, 54, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
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: REAL300025277860 none O=C(CC1OCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 49, 49, 49, 49, 49, 65, 65, 89, 130, 201, 201, 201, 201, 201, 49, 49, 6, 6, 1, 1, 1, 1, 1, 1, 1, 16, 49, 49, 49, 49, 49, 49, 89, 89, 201, 49, 49, 49] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025277860 none O=C(CC1OCCCO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 199, 201, 201, 201, 201, 201, 54, 54, 54, 54, 54, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 199, 199, 201, 201, 201, 201, 201, 201, 201, 127, 54, 54, 54, 54, 54, 54, 29, 29, 1, 54, 54, 54] 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])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277860 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277860
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277860/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277860
Building REAL300025277861
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277861'
/scratch/stefan/7808390/working/building/REAL300025277861 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277861

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277861/0 /scratch/stefan/7808390/working/building/REAL300025277861 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/748
`/scratch/stefan/7808390/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1)

`REAL300025277861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277861 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 57, 57, 57, 57, 57, 1, 1, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 10, 10, 57, 1, 1, 1, 10] 90
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277861 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 16, 16, 35, 52, 90, 90, 90, 90, 90, 10, 10, 1, 1, 2, 2, 2, 1, 5, 10, 10, 10, 10, 10, 10, 35, 35, 90, 10, 10, 10, 1] 90
rigid atoms, others: [0, 1, 2, 3, 4, 43, 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: 251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277861 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 72, 72, 72, 57, 57, 57, 57, 57, 51, 42, 51, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 90, 90, 90, 90, 90, 90, 72, 57, 57, 57, 57, 57, 57, 42, 42, 1, 57, 57, 57, 90] 90
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: 277
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277861 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277861
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277861/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277861
Building REAL300025277862
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277862'
/scratch/stefan/7808390/working/building/REAL300025277862 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277862

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277862/0 /scratch/stefan/7808390/working/building/REAL300025277862 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/749
`/scratch/stefan/7808390/working/3D/749' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N(C)C=C1)

`REAL300025277862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277862 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N(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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 14, 64, 64, 64, 64, 64, 1, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 9, 9, 64, 1, 1, 1, 18, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47])
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: REAL300025277862 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N(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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 18, 18, 18, 18, 18, 31, 31, 62, 98, 201, 201, 201, 201, 201, 18, 18, 1, 1, 1, 1, 2, 2, 2, 5, 18, 18, 18, 18, 18, 18, 62, 62, 201, 18, 18, 18, 2, 2, 2, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 46, 47, 23, 24, 25, 26] set([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, 42, 43, 44, 45])
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: REAL300025277862 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N(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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 100, 100, 100, 64, 64, 64, 64, 64, 46, 40, 46, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 100, 64, 64, 64, 64, 64, 64, 40, 40, 1, 64, 64, 64, 201, 201, 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, 47])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277862 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277862
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277862/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277862
Building REAL300025277863
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277863'
/scratch/stefan/7808390/working/building/REAL300025277863 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277863

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277863/0 /scratch/stefan/7808390/working/building/REAL300025277863 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/750
`/scratch/stefan/7808390/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CN=N1)

`REAL300025277863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277863 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 19, 62, 62, 62, 62, 62, 1, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 9, 9, 62, 1, 1, 1, 19] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277863 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in 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, 19, 19, 19, 19, 19, 31, 31, 69, 107, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 2, 2, 2, 1, 5, 19, 19, 19, 19, 19, 19, 69, 69, 201, 19, 19, 19, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25, 26, 30] set([5, 6, 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])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277863 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 92, 92, 92, 62, 62, 62, 62, 62, 40, 34, 40, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 92, 62, 62, 62, 62, 62, 62, 34, 34, 1, 62, 62, 62, 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])
total number of confs: 455
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277863 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277863
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277863/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277863
Building REAL300025277864
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277864'
/scratch/stefan/7808390/working/building/REAL300025277864 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277864

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277864/0 /scratch/stefan/7808390/working/building/REAL300025277864 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/751
`/scratch/stefan/7808390/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277864 none O=C(CCN1C=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 27, 27, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 34, 34, 34, 34, 34, 1, 1, 27, 27, 27, 27, 36, 36, 6, 1, 1, 1, 1, 1, 1, 5, 5, 34, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277864 none O=C(CCN1C=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 9, 5, 1, 1, 1, 1, 1, 1, 15, 15, 36, 36, 36, 36, 36, 47, 47, 70, 109, 201, 201, 201, 201, 201, 36, 36, 9, 9, 5, 5, 1, 1, 15, 36, 36, 36, 36, 36, 36, 70, 70, 201, 36, 36, 36] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277864 none O=C(CCN1C=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [101, 101, 101, 197, 197, 201, 201, 201, 201, 34, 34, 34, 34, 34, 22, 17, 22, 10, 1, 1, 1, 1, 1, 1, 1, 34, 34, 197, 197, 197, 197, 201, 201, 101, 34, 34, 34, 34, 34, 34, 17, 17, 1, 34, 34, 34] 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])
total number of confs: 705
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277864 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277864
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277864/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277864
Building REAL300025277865
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277865'
/scratch/stefan/7808390/working/building/REAL300025277865 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277865

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277865/0 /scratch/stefan/7808390/working/building/REAL300025277865 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/752
`/scratch/stefan/7808390/working/3D/752' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277865 none CC(=O)N1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 30, 51, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 32, 32, 32, 32, 32, 1, 1, 30, 51, 51, 51, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 5, 5, 32, 1, 1, 1, 30, 30] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277865 none CC(=O)N1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 8, 8, 30, 30, 30, 30, 30, 40, 40, 62, 96, 166, 166, 166, 166, 166, 30, 30, 1, 2, 2, 2, 1, 1, 1, 8, 30, 30, 30, 30, 30, 30, 62, 62, 166, 30, 30, 30, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 46, 47, 26, 30, 31] set([0, 2, 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: 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: REAL300025277865 none CC(=O)N1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 166, 201, 166, 166, 79, 79, 79, 32, 32, 32, 32, 32, 22, 19, 22, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 166, 201, 201, 201, 166, 166, 166, 79, 32, 32, 32, 32, 32, 32, 19, 19, 1, 32, 32, 32, 166, 166] 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: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277865 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277865
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277865/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277865
Building REAL300025277866
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277866'
/scratch/stefan/7808390/working/building/REAL300025277866 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277866

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277866/0 /scratch/stefan/7808390/working/building/REAL300025277866 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/753
`/scratch/stefan/7808390/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC1=O)

`REAL300025277866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277866 none CN1OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [22, 22, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 42, 113, 113, 113, 113, 113, 1, 1, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 24, 24, 113, 1, 1, 1, 22] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
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: REAL300025277866 none CN1OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 22, 22, 22, 22, 22, 46, 46, 113, 152, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 113, 113, 201, 22, 22, 22, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 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])
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: REAL300025277866 none CN1OC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 195, 195, 195, 113, 113, 113, 113, 113, 73, 40, 73, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 195, 113, 113, 113, 113, 113, 113, 40, 40, 1, 113, 113, 113, 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: 626
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277866 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277866
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277866/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277866
Building REAL300025277867
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277867'
/scratch/stefan/7808390/working/building/REAL300025277867 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277867

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277867/0 /scratch/stefan/7808390/working/building/REAL300025277867 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/754
`/scratch/stefan/7808390/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277867 none CCC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 79, 79, 79, 33, 33, 33, 33, 33, 24, 21, 24, 10, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 33, 33, 33, 33, 33, 33, 21, 21, 1, 33, 33, 33] 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])
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: REAL300025277867 none CCC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 31, 52, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 33, 33, 33, 33, 33, 1, 1, 53, 53, 53, 53, 53, 52, 52, 52, 52, 31, 31, 6, 1, 1, 1, 1, 1, 1, 4, 4, 33, 1, 1, 1] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277867 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277867
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277867/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277867
Building REAL300025277868
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277868'
/scratch/stefan/7808390/working/building/REAL300025277868 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277868

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277868/0 /scratch/stefan/7808390/working/building/REAL300025277868 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/755
`/scratch/stefan/7808390/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1)

`REAL300025277868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277868 none COC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 55, 55, 55, 55, 55, 1, 1, 33, 33, 33, 33, 33, 33, 27, 27, 4, 1, 1, 1, 1, 1, 1, 6, 6, 55, 1, 1, 1, 33, 33, 33, 33, 33, 33] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49, 50])
total number of confs: 190
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277868 none COC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 15, 15, 15, 33, 33, 33, 33, 33, 48, 48, 72, 107, 201, 201, 201, 201, 201, 33, 33, 1, 1, 1, 4, 4, 4, 5, 5, 15, 33, 33, 33, 33, 33, 33, 72, 72, 201, 33, 33, 33, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 49, 50, 24, 25, 26] set([0, 4, 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])
total number of confs: 532
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: REAL300025277868 none COC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 97, 97, 97, 55, 55, 55, 55, 55, 36, 27, 36, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 195, 195, 97, 55, 55, 55, 55, 55, 55, 27, 27, 1, 55, 55, 55, 201, 201, 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, 50])
total number of confs: 759
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277868 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277868
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277868/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277868
Building REAL300025277869
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277869'
/scratch/stefan/7808390/working/building/REAL300025277869 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277869

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277869/0 /scratch/stefan/7808390/working/building/REAL300025277869 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/756
`/scratch/stefan/7808390/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277869 none CC1OCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 8, 8, 8, 8, 8, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 4, 4, 8, 1, 1, 1] 12
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277869 none CC1OCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 6, 6, 6, 6, 6, 7, 7, 8, 9, 12, 12, 12, 12, 12, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 8, 8, 12, 6, 6, 6] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277869 none CC1OCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8, 8] 12
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])
total number of confs: 30
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277869 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277869
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277869/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277869
Building REAL300025277870
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277870'
/scratch/stefan/7808390/working/building/REAL300025277870 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277870

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277870/0 /scratch/stefan/7808390/working/building/REAL300025277870 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/757
`/scratch/stefan/7808390/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277870 none C#CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 159, 169, 56, 56, 56, 26, 26, 26, 26, 26, 19, 18, 19, 9, 1, 1, 1, 1, 1, 1, 1, 26, 26, 201, 186, 187, 188, 188, 169, 169, 56, 26, 26, 26, 26, 26, 26, 18, 18, 1, 26, 26, 26] 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])
total number of confs: 959
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277870 none C#CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 41, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 26, 26, 26, 26, 26, 1, 1, 59, 55, 55, 49, 49, 32, 32, 6, 1, 1, 1, 1, 1, 1, 4, 4, 26, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277870 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277870
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277870/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277870
Building REAL300025277871
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277871'
/scratch/stefan/7808390/working/building/REAL300025277871 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277871

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277871/0 /scratch/stefan/7808390/working/building/REAL300025277871 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/758
`/scratch/stefan/7808390/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(Cl)OC=C3)C2C1)

`REAL300025277871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277871 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(Cl)OC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 21, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 1, 1, 12, 12, 80, 1, 1, 1, 1, 1, 1, 4, 13, 13, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 40, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277871 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(Cl)OC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 40, 13, 1, 1, 1, 1, 1, 1, 1, 58, 80, 80, 80, 80, 80, 118, 118, 118, 201, 201, 201, 201, 201, 80, 80, 40, 40, 1, 80, 80, 80, 80, 80, 80, 118, 201, 201, 80, 80, 80] 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])
total number of confs: 511
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: REAL300025277871 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(Cl)OC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 13, 25, 62, 95, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 62, 62, 201, 13, 13, 13, 13, 13, 13, 5, 1, 1, 13, 13, 13] 201
rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 487
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277871 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277871
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277871/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277871
Building REAL300025277872
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277872'
/scratch/stefan/7808390/working/building/REAL300025277872 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277872

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277872/0 /scratch/stefan/7808390/working/building/REAL300025277872 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/759
`/scratch/stefan/7808390/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NS1)

`REAL300025277872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277872 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 48, 119, 119, 119, 119, 119, 1, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 28, 28, 119, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 261
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277872 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 3, 3, 3, 11, 11, 11, 11, 11, 30, 30, 88, 126, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 11, 11, 88, 88, 201, 11, 11, 11] 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: 541
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277872 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 119, 119, 119, 119, 119, 72, 41, 72, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 41, 41, 1, 119, 119, 119] 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])
total number of confs: 599
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277872 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277872
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277872/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277872
Building REAL300025277873
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277873'
/scratch/stefan/7808390/working/building/REAL300025277873 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277873

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277873/0 /scratch/stefan/7808390/working/building/REAL300025277873 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/760
`/scratch/stefan/7808390/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277873 none CCN1C=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 10, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 73, 73, 73, 73, 73, 1, 1, 16, 16, 16, 16, 16, 10, 10, 6, 1, 1, 1, 1, 1, 1, 6, 6, 73, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025277873 none CCN1C=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 10, 10, 10, 10, 10, 16, 16, 30, 50, 120, 120, 120, 120, 120, 10, 10, 3, 3, 3, 3, 3, 1, 1, 3, 10, 10, 10, 10, 10, 10, 30, 30, 120, 10, 10, 10] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 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: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277873 none CCN1C=CN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 120, 120, 120, 120, 120, 120, 120, 120, 73, 73, 73, 73, 73, 44, 31, 44, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 120, 120, 120, 73, 73, 73, 73, 73, 73, 31, 31, 1, 73, 73, 73] 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])
total number of confs: 880
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277873 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277873
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277873/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277873
Building REAL300025277874
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277874'
/scratch/stefan/7808390/working/building/REAL300025277874 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277874

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277874/0 /scratch/stefan/7808390/working/building/REAL300025277874 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/761
`/scratch/stefan/7808390/working/3D/761' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOCC3)C2C1)

`REAL300025277874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277874 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 10, 16, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 1, 1, 10, 10, 66, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277874 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 47, 66, 66, 66, 66, 66, 124, 124, 124, 201, 201, 201, 201, 201, 201, 66, 66, 38, 38, 1, 66, 66, 66, 66, 66, 66, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66] 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: 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: REAL300025277874 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 26, 36, 71, 110, 201, 201, 201, 201, 201, 26, 26, 26, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 26, 26, 71, 71, 201, 26, 26, 26, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 503
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277874 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277874
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277874/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277874
Building REAL300025277875
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277875'
/scratch/stefan/7808390/working/building/REAL300025277875 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277875

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277875/0 /scratch/stefan/7808390/working/building/REAL300025277875 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/762
`/scratch/stefan/7808390/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NC=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277875 none O=C(CCC1=NC=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 66, 66, 66, 66, 66, 1, 1, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 9, 9, 66, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277875 none O=C(CCC1=NC=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 5, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 41, 41, 61, 107, 201, 201, 201, 201, 201, 27, 27, 5, 5, 5, 5, 1, 1, 1, 7, 27, 27, 27, 27, 27, 27, 61, 61, 201, 27, 27, 27] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277875 none O=C(CCC1=NC=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [149, 149, 149, 201, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 149, 66, 66, 66, 66, 66, 66, 28, 28, 1, 66, 66, 66] 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])
total number of confs: 720
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277875 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277875
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277875/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277875
Building REAL300025277876
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277876'
/scratch/stefan/7808390/working/building/REAL300025277876 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277876

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277876/0 /scratch/stefan/7808390/working/building/REAL300025277876 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/763
`/scratch/stefan/7808390/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(O)CC3)C2C1)

`REAL300025277876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277876 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(O)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 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, 16, 25, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 30, 1, 1, 16, 16, 72, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 90, 30, 30, 30, 30, 1, 1, 1] 603
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277876 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(O)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [46, 36, 13, 1, 1, 1, 1, 1, 1, 1, 46, 72, 72, 72, 72, 72, 142, 142, 142, 201, 201, 201, 201, 201, 201, 72, 72, 36, 36, 1, 72, 72, 72, 72, 72, 72, 142, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 201, 72, 72, 72] 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])
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: REAL300025277876 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(O)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [56, 30, 56, 116, 152, 201, 201, 201, 201, 201, 30, 30, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 30, 30, 116, 116, 201, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 30, 30, 30] 603
rigid atoms, others: [37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 48, 49, 50])
total number of confs: 603
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277876 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277876
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277876/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277876
Building REAL300025277877
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277877'
/scratch/stefan/7808390/working/building/REAL300025277877 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277877

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277877/0 /scratch/stefan/7808390/working/building/REAL300025277877 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/764
`/scratch/stefan/7808390/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277877 none CC(C)(O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [198, 201, 201, 201, 120, 120, 120, 55, 55, 55, 55, 55, 38, 30, 38, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 603, 201, 201, 120, 55, 55, 55, 55, 55, 55, 30, 30, 1, 55, 55, 55] 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])
total number of confs: 1379
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: REAL300025277877 none CC(C)(O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [28, 30, 29, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 55, 55, 55, 55, 55, 1, 1, 32, 32, 32, 32, 32, 32, 96, 30, 30, 6, 1, 1, 1, 1, 1, 1, 6, 6, 55, 1, 1, 1] 603
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 339
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277877 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277877
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277877/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277877
Building REAL300025277878
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277878'
/scratch/stefan/7808390/working/building/REAL300025277878 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277878

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277878/0 /scratch/stefan/7808390/working/building/REAL300025277878 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/765
`/scratch/stefan/7808390/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277878 none CC1=CC=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 22, 6, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 25, 67, 67, 67, 67, 67, 1, 1, 22, 22, 22, 22, 7, 22, 6, 1, 1, 1, 1, 1, 1, 17, 17, 67, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277878 none CC1=CC=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 1, 7, 7, 7, 22, 22, 22, 22, 22, 44, 44, 112, 145, 201, 201, 201, 201, 201, 22, 22, 1, 2, 2, 2, 1, 1, 7, 22, 22, 22, 22, 22, 22, 112, 112, 201, 22, 22, 22] 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])
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: REAL300025277878 none CC1=CC=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 119, 201, 201, 119, 119, 119, 67, 67, 67, 67, 67, 45, 36, 45, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 186, 201, 119, 67, 67, 67, 67, 67, 67, 36, 36, 1, 67, 67, 67] 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])
total number of confs: 915
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277878 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277878
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277878/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277878
Building REAL300025277879
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277879'
/scratch/stefan/7808390/working/building/REAL300025277879 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277879

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277879/0 /scratch/stefan/7808390/working/building/REAL300025277879 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/766
`/scratch/stefan/7808390/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277879 none COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [179, 179, 153, 153, 153, 71, 71, 71, 71, 71, 47, 37, 47, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 179, 201, 201, 179, 179, 179, 179, 153, 71, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71, 71, 201, 201, 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, 47])
total number of confs: 715
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277879 none COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 71, 71, 71, 71, 71, 1, 1, 15, 26, 26, 18, 18, 18, 15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 71, 1, 1, 1, 26, 26, 26, 26, 26] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47])
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: REAL300025277879 none COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 9, 9, 9, 26, 26, 26, 26, 26, 37, 37, 63, 100, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 7, 7, 7, 4, 9, 26, 26, 26, 26, 26, 26, 63, 63, 201, 26, 26, 26, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 43, 44, 45, 46, 47, 23, 24, 25] set([0, 1, 3, 4, 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])
total number of confs: 506
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277879 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277879
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277879/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277879
Building REAL300025277880
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277880'
/scratch/stefan/7808390/working/building/REAL300025277880 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277880

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277880/0 /scratch/stefan/7808390/working/building/REAL300025277880 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/767
`/scratch/stefan/7808390/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1)

`REAL300025277880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277880 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [32, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 18, 80, 80, 80, 80, 80, 1, 1, 14, 14, 14, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 11, 11, 80, 1, 1, 1, 14, 13] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46])
total number of confs: 235
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: REAL300025277880 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 24, 24, 51, 81, 181, 181, 181, 181, 181, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 6, 14, 14, 14, 14, 14, 14, 51, 51, 181, 14, 14, 14, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 45, 46, 24, 25, 26] set([0, 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])
total number of confs: 429
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: REAL300025277880 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 181, 181, 128, 128, 128, 80, 80, 80, 80, 80, 52, 31, 52, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 181, 181, 181, 201, 201, 201, 201, 201, 128, 80, 80, 80, 80, 80, 80, 31, 31, 1, 80, 80, 80, 181, 181] 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])
total number of confs: 615
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277880 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277880
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277880/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277880
Building REAL300025277881
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277881'
/scratch/stefan/7808390/working/building/REAL300025277881 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277881

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277881/0 /scratch/stefan/7808390/working/building/REAL300025277881 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/768
`/scratch/stefan/7808390/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277881 none CN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 75, 75, 75, 75, 75, 1, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 11, 11, 75, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277881 none CN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 15, 15, 15, 15, 15, 26, 26, 70, 109, 201, 201, 201, 201, 201, 15, 15, 2, 2, 2, 1, 5, 15, 15, 15, 15, 15, 15, 70, 70, 201, 15, 15, 15] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 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: 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: REAL300025277881 none CN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 200, 200, 200, 75, 75, 75, 75, 75, 48, 36, 48, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 200, 75, 75, 75, 75, 75, 75, 36, 36, 1, 75, 75, 75] 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])
total number of confs: 592
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277881 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277881
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277881/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277881
Building REAL300025277882
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277882'
/scratch/stefan/7808390/working/building/REAL300025277882 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277882

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277882/0 /scratch/stefan/7808390/working/building/REAL300025277882 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/769
`/scratch/stefan/7808390/working/3D/769' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277882 none CCCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 75, 168, 75, 75, 27, 27, 27, 27, 27, 19, 16, 19, 10, 1, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168, 75, 27, 27, 27, 27, 27, 27, 16, 16, 1, 27, 27, 27] 201
rigid atoms, others: [48, 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, 49, 50, 51])
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: REAL300025277882 none CCCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 27, 27, 27, 27, 27, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 5, 5, 27, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277882 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277882
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277882/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277882
Building REAL300025277883
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277883'
/scratch/stefan/7808390/working/building/REAL300025277883 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277883

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277883/0 /scratch/stefan/7808390/working/building/REAL300025277883 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/770
`/scratch/stefan/7808390/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277883 none CC1CC(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 29, 29, 29, 29, 29, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 9, 9, 29, 1, 1, 1] 46
rigid atoms, others: [43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 50, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277883 none CC1CC(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 12, 12, 16, 16, 29, 36, 46, 46, 46, 46, 46, 12, 12, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 8, 12, 12, 12, 12, 12, 12, 29, 29, 46, 12, 12, 12] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 26, 37, 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, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277883 none CC1CC(C)C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 42, 42, 42, 29, 29, 29, 29, 29, 25, 22, 25, 12, 1, 1, 1, 1, 1, 1, 1, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 42, 29, 29, 29, 29, 29, 29, 22, 22, 1, 29, 29, 29] 46
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])
total number of confs: 141
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277883 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277883
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277883/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277883
Building REAL300025277884
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277884'
/scratch/stefan/7808390/working/building/REAL300025277884 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277884

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277884/0 /scratch/stefan/7808390/working/building/REAL300025277884 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/771
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)[C@H]3C[C@@H]3C(F)F)C2C1)

`REAL300025277884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277884 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3C[C@@H]3C(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 6, 10, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 47, 47, 1, 1, 6, 6, 49, 1, 1, 1, 1, 1, 1, 6, 28, 28, 47, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 41, 10, 11, 12, 13, 14, 15, 43, 26, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40])
total number of confs: 244
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277884 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3C[C@@H]3C(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 27, 12, 1, 1, 1, 1, 1, 1, 1, 33, 49, 49, 49, 49, 49, 105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 49, 49, 27, 27, 1, 49, 49, 49, 49, 49, 49, 105, 201, 201, 201, 49, 49, 49] 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: 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: REAL300025277884 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3C[C@@H]3C(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 28, 38, 58, 90, 201, 201, 201, 201, 201, 28, 28, 28, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 5, 5, 28, 28, 58, 58, 201, 28, 28, 28, 28, 28, 28, 10, 1, 1, 5, 28, 28, 28] 201
rigid atoms, others: [38, 39, 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, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 479
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277884 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277884
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277884/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277884
Building REAL300025277885
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277885'
/scratch/stefan/7808390/working/building/REAL300025277885 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277885

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277885/0 /scratch/stefan/7808390/working/building/REAL300025277885 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/772
`/scratch/stefan/7808390/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277885 none CC1=COC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [27, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 59, 59, 59, 59, 59, 1, 1, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 8, 8, 59, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025277885 none CC1=COC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 27, 27, 27, 27, 27, 36, 36, 72, 112, 201, 201, 201, 201, 201, 27, 27, 2, 2, 2, 1, 2, 2, 2, 7, 27, 27, 27, 27, 27, 27, 72, 72, 201, 27, 27, 27] 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])
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: REAL300025277885 none CC1=COC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 101, 101, 101, 59, 59, 59, 59, 59, 44, 39, 44, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 101, 59, 59, 59, 59, 59, 59, 39, 39, 1, 59, 59, 59] 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])
total number of confs: 466
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277885 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277885
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277885/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277885
Building REAL300025277886
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277886'
/scratch/stefan/7808390/working/building/REAL300025277886 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277886

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277886/0 /scratch/stefan/7808390/working/building/REAL300025277886 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/773
`/scratch/stefan/7808390/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277886 none CC1(C)CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 17, 47, 47, 47, 47, 47, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 13, 13, 47, 1, 1, 1, 32, 32] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 24, 39, 47, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 48, 49])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277886 none CC1(C)CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 32, 32, 32, 32, 32, 50, 50, 108, 143, 201, 201, 201, 201, 201, 32, 32, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 108, 108, 201, 32, 32, 32, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 48, 49, 25, 5] 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277886 none CC1(C)CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 79, 79, 79, 47, 47, 47, 47, 47, 31, 31, 31, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 47, 47, 47, 47, 47, 47, 31, 31, 1, 47, 47, 47, 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])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277886 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277886
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277886/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277886
Building REAL300025277887
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277887'
/scratch/stefan/7808390/working/building/REAL300025277887 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277887

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277887/0 /scratch/stefan/7808390/working/building/REAL300025277887 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/774
`/scratch/stefan/7808390/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277887 none CC(C)[C@@H](O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 191, 201, 158, 191, 191, 158, 158, 64, 64, 64, 64, 64, 38, 31, 38, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 573, 158, 64, 64, 64, 64, 64, 64, 31, 31, 1, 64, 64, 64] 603
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])
total number of confs: 1267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277887 none CC(C)[C@@H](O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [28, 17, 28, 6, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 64, 64, 64, 64, 64, 1, 1, 28, 28, 28, 28, 28, 28, 28, 51, 6, 1, 1, 1, 1, 1, 1, 7, 7, 64, 1, 1, 1] 603
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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
/scratch/stefan/7808390/working/building/REAL300025277887 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277887
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277887/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277887
Building REAL300025277888
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277888'
/scratch/stefan/7808390/working/building/REAL300025277888 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277888

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277888/0 /scratch/stefan/7808390/working/building/REAL300025277888 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/775
`/scratch/stefan/7808390/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277888 none CCOC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 20, 20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 66, 66, 66, 66, 66, 1, 1, 20, 43, 43, 43, 43, 43, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 7, 7, 66, 1, 1, 1, 20, 20] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50])
total number of confs: 185
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277888 none CCOC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 6, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 31, 31, 56, 94, 199, 199, 199, 199, 199, 20, 20, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 11, 20, 20, 20, 20, 20, 20, 56, 56, 199, 20, 20, 20, 1, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 49, 50, 35, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 473
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: REAL300025277888 none CCOC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 199, 199, 103, 103, 103, 66, 66, 66, 66, 66, 53, 31, 53, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199, 103, 66, 66, 66, 66, 66, 66, 31, 31, 1, 66, 66, 66, 199, 199] 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])
total number of confs: 658
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277888 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277888
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277888/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277888
Building REAL300025277889
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277889'
/scratch/stefan/7808390/working/building/REAL300025277889 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277889

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277889/0 /scratch/stefan/7808390/working/building/REAL300025277889 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/776
`/scratch/stefan/7808390/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1)

`REAL300025277889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277889 none CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 52, 52, 52, 52, 52, 1, 1, 33, 33, 33, 33, 33, 33, 33, 20, 20, 6, 1, 1, 1, 1, 1, 1, 5, 5, 52, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 44, 43, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277889 none CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 33, 33, 33, 33, 33, 44, 44, 66, 110, 201, 201, 201, 201, 201, 33, 33, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 33, 33, 33, 33, 33, 33, 66, 66, 201, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([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, 42, 43, 44])
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: REAL300025277889 none CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 115, 115, 115, 52, 52, 52, 52, 52, 35, 28, 35, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 155, 155, 115, 52, 52, 52, 52, 52, 52, 28, 28, 1, 52, 52, 52, 201, 201, 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, 52])
total number of confs: 771
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277889 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277889
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277889/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277889
Building REAL300025277890
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277890'
/scratch/stefan/7808390/working/building/REAL300025277890 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277890

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277890/0 /scratch/stefan/7808390/working/building/REAL300025277890 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/777
`/scratch/stefan/7808390/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=N1)

`REAL300025277890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277890 none CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 48, 126, 126, 126, 126, 126, 1, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 28, 28, 126, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277890 none CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 3, 3, 3, 11, 11, 11, 11, 11, 32, 32, 101, 144, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 11, 11, 101, 101, 201, 11, 11, 11] 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: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277890 none CN1C=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 126, 126, 126, 126, 126, 81, 42, 81, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 126, 42, 42, 1, 126, 126, 126] 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])
total number of confs: 638
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277890 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277890
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277890/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277890
Building REAL300025277891
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277891'
/scratch/stefan/7808390/working/building/REAL300025277891 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277891

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277891/0 /scratch/stefan/7808390/working/building/REAL300025277891 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/778
`/scratch/stefan/7808390/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277891 none CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 43, 43, 43, 43, 43, 1, 1, 39, 39, 39, 39, 28, 28, 6, 1, 1, 1, 1, 1, 1, 5, 5, 43, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277891 none CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 4, 13, 13, 13, 39, 39, 39, 39, 39, 54, 54, 75, 111, 201, 201, 201, 201, 201, 39, 39, 1, 2, 2, 2, 4, 4, 13, 39, 39, 39, 39, 39, 39, 75, 75, 201, 39, 39, 39] 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: 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: REAL300025277891 none CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 104, 104, 104, 43, 43, 43, 43, 43, 28, 24, 28, 11, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 201, 104, 43, 43, 43, 43, 43, 43, 24, 24, 1, 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])
total number of confs: 748
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277891 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277891
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277891/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277891
Building REAL300025277892
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277892'
/scratch/stefan/7808390/working/building/REAL300025277892 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277892

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277892/0 /scratch/stefan/7808390/working/building/REAL300025277892 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/779
`/scratch/stefan/7808390/working/3D/779' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277892 none CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 35, 91, 91, 91, 91, 91, 1, 1, 15, 15, 15, 15, 14, 6, 1, 1, 1, 1, 1, 1, 22, 22, 91, 1, 1, 1] 193
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 209
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: REAL300025277892 none CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
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, 7, 7, 7, 15, 15, 15, 15, 15, 37, 37, 91, 130, 193, 193, 193, 193, 193, 15, 15, 1, 2, 2, 2, 1, 7, 15, 15, 15, 15, 15, 15, 91, 91, 193, 15, 15, 15] 193
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])
total number of confs: 529
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: REAL300025277892 none CN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
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, 136, 136, 136, 91, 91, 91, 91, 91, 64, 39, 64, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 193, 193, 193, 193, 193, 136, 91, 91, 91, 91, 91, 91, 39, 39, 1, 91, 91, 91] 193
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])
total number of confs: 537
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277892 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277892
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277892/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277892
Building REAL300025277893
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277893'
/scratch/stefan/7808390/working/building/REAL300025277893 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277893

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277893/0 /scratch/stefan/7808390/working/building/REAL300025277893 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/780
`/scratch/stefan/7808390/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277893 none CNC(=O)NCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 69, 69, 69, 26, 26, 26, 26, 26, 21, 17, 21, 10, 1, 1, 1, 1, 1, 1, 1, 26, 26, 201, 201, 201, 201, 201, 201, 201, 190, 190, 69, 26, 26, 26, 26, 26, 26, 17, 17, 1, 26, 26, 26] 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])
total number of confs: 783
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277893 none CNC(=O)NCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 44, 44, 34, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 26, 26, 26, 26, 26, 1, 1, 44, 44, 44, 44, 44, 44, 44, 34, 34, 5, 1, 1, 1, 1, 1, 1, 4, 4, 26, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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
/scratch/stefan/7808390/working/building/REAL300025277893 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277893
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277893/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277893
Building REAL300025277894
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277894'
/scratch/stefan/7808390/working/building/REAL300025277894 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277894

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277894/0 /scratch/stefan/7808390/working/building/REAL300025277894 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/781
`/scratch/stefan/7808390/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(F)C=CS3)C2C1)

`REAL300025277894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277894 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(F)C=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.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, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 14, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 1, 9, 9, 56, 1, 1, 1, 1, 1, 1, 6, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 40, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277894 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(F)C=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.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, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 41, 56, 56, 56, 56, 56, 114, 114, 114, 201, 201, 201, 201, 201, 56, 56, 35, 35, 1, 56, 56, 56, 56, 56, 56, 114, 201, 201, 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])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277894 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=C(F)C=CS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.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, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 30, 67, 104, 201, 201, 201, 201, 201, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 67, 67, 201, 20, 20, 20, 20, 20, 20, 6, 1, 1, 20, 20, 20] 201
rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 498
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277894 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277894
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277894/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277894
Building REAL300025277895
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277895'
/scratch/stefan/7808390/working/building/REAL300025277895 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277895

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277895/0 /scratch/stefan/7808390/working/building/REAL300025277895 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/782
`/scratch/stefan/7808390/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277895 none CCN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 83, 83, 83, 83, 83, 1, 1, 10, 29, 29, 29, 29, 29, 10, 6, 1, 1, 1, 1, 1, 1, 7, 7, 83, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
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: REAL300025277895 none CCN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 16, 16, 34, 65, 168, 168, 168, 168, 168, 10, 10, 1, 7, 7, 7, 7, 7, 1, 4, 10, 10, 10, 10, 10, 10, 34, 34, 168, 10, 10, 10] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025277895 none CCN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 168, 168, 168, 168, 166, 166, 166, 83, 83, 83, 83, 83, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 168, 201, 201, 201, 201, 201, 168, 166, 83, 83, 83, 83, 83, 83, 31, 31, 1, 83, 83, 83] 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])
total number of confs: 728
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277895 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277895
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277895/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277895
Building REAL300025277896
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277896'
/scratch/stefan/7808390/working/building/REAL300025277896 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277896

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277896/0 /scratch/stefan/7808390/working/building/REAL300025277896 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/783
`/scratch/stefan/7808390/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277896 none CC(C)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 125, 159, 95, 95, 95, 50, 50, 50, 50, 50, 38, 32, 38, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 159, 201, 201, 159, 159, 159, 159, 159, 159, 125, 125, 95, 50, 50, 50, 50, 50, 50, 32, 32, 1, 50, 50, 50, 201, 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: 805
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: REAL300025277896 none CC(C)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 11, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 50, 50, 50, 50, 50, 1, 1, 25, 46, 46, 25, 25, 25, 25, 25, 25, 11, 11, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 1, 1, 1, 46, 46, 46, 46, 46] 201
rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 46, 47, 40, 41, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 48, 49, 50, 51, 52])
total number of confs: 263
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277896 none CC(C)(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 9, 15, 15, 15, 46, 46, 46, 46, 46, 55, 55, 78, 100, 201, 201, 201, 201, 201, 46, 46, 1, 1, 1, 7, 7, 7, 7, 7, 7, 9, 9, 15, 46, 46, 46, 46, 46, 46, 78, 78, 201, 46, 46, 46, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 2, 3, 4, 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: 525
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277896 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277896
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277896/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277896
Building REAL300025277897
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277897'
/scratch/stefan/7808390/working/building/REAL300025277897 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277897

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277897/0 /scratch/stefan/7808390/working/building/REAL300025277897 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/784
`/scratch/stefan/7808390/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277897 none CCN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 53, 53, 53, 53, 53, 1, 1, 25, 25, 25, 25, 25, 14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 53, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 164
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277897 none CCN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 4, 4, 4, 14, 14, 14, 14, 14, 22, 22, 37, 64, 120, 120, 120, 120, 120, 14, 14, 4, 4, 4, 4, 4, 1, 4, 14, 14, 14, 14, 14, 14, 37, 37, 120, 14, 14, 14] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 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: 324
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277897 none CCN1N=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 120, 120, 120, 120, 120, 117, 117, 117, 53, 53, 53, 53, 53, 36, 27, 36, 12, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 120, 117, 53, 53, 53, 53, 53, 53, 27, 27, 1, 53, 53, 53] 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])
total number of confs: 848
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277897 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277897
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277897/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277897
Building REAL300025277898
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277898'
/scratch/stefan/7808390/working/building/REAL300025277898 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277898

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277898/0 /scratch/stefan/7808390/working/building/REAL300025277898 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/785
`/scratch/stefan/7808390/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025277898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277898 none CC1=CSC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 50, 50, 50, 50, 50, 1, 1, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 13, 13, 50, 1, 1, 1, 12] 85
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 115
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277898 none CC1=CSC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 23, 23, 37, 54, 85, 85, 85, 85, 85, 12, 12, 1, 2, 2, 2, 1, 7, 12, 12, 12, 12, 12, 12, 37, 37, 85, 12, 12, 12, 1] 85
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: 231
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277898 none CC1=CSC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 85, 77, 77, 77, 50, 50, 50, 50, 50, 38, 31, 38, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 85, 85, 85, 85, 85, 77, 50, 50, 50, 50, 50, 50, 31, 31, 1, 50, 50, 50, 85] 85
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: 257
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277898 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277898
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277898/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277898
Building REAL300025277899
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277899'
/scratch/stefan/7808390/working/building/REAL300025277899 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277899

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277899/0 /scratch/stefan/7808390/working/building/REAL300025277899 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/786
`/scratch/stefan/7808390/working/3D/786' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3(F)F)C2C1)

`REAL300025277899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277899 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 15, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 1, 1, 9, 9, 56, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 1, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 40, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277899 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 35, 13, 1, 1, 1, 1, 1, 1, 1, 40, 56, 56, 56, 56, 56, 119, 119, 119, 201, 201, 201, 201, 56, 56, 35, 35, 1, 56, 56, 56, 56, 56, 56, 119, 201, 201, 201, 56, 56, 56] 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: 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: REAL300025277899 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC3(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 30, 40, 77, 118, 201, 201, 201, 201, 201, 30, 30, 30, 30, 10, 10, 1, 10, 1, 1, 1, 1, 1, 30, 30, 77, 77, 201, 30, 30, 30, 30, 30, 30, 10, 1, 1, 1, 30, 30, 30] 201
rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 534
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277899 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277899
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277899/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277899
Building REAL300025277900
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277900'
/scratch/stefan/7808390/working/building/REAL300025277900 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277900

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277900/0 /scratch/stefan/7808390/working/building/REAL300025277900 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/787
`/scratch/stefan/7808390/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277900 none CCC(C)=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 105, 105, 105, 64, 64, 64, 33, 33, 33, 33, 33, 22, 18, 22, 11, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 105, 105, 105, 105, 64, 33, 33, 33, 33, 33, 33, 18, 18, 1, 33, 33, 33] 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])
total number of confs: 929
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277900 none CCC(C)=CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 33, 33, 33, 33, 33, 1, 1, 34, 34, 34, 34, 34, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 5, 5, 33, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277900 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277900
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277900/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277900
Building REAL300025277901
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277901'
/scratch/stefan/7808390/working/building/REAL300025277901 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277901

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277901/0 /scratch/stefan/7808390/working/building/REAL300025277901 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/788
`/scratch/stefan/7808390/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277901 none CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [29, 29, 29, 6, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 13, 41, 41, 41, 41, 41, 1, 1, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 8, 8, 41, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277901 none CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 9, 9, 9, 29, 29, 29, 29, 29, 39, 39, 75, 114, 201, 201, 201, 201, 201, 29, 29, 2, 2, 2, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 75, 75, 201, 29, 29, 29] 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: 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: REAL300025277901 none CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 130, 201, 201, 98, 98, 98, 41, 41, 41, 41, 41, 28, 25, 28, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 201, 98, 41, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41, 41] 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])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277901 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277901
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277901/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277901
Building REAL300025277902
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277902'
/scratch/stefan/7808390/working/building/REAL300025277902 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277902

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277902/0 /scratch/stefan/7808390/working/building/REAL300025277902 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/789
`/scratch/stefan/7808390/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C#CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277902 none CC(C)C#CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 125, 125, 125, 125, 125, 84, 56, 84, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 125, 56, 56, 1, 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])
total number of confs: 629
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277902 none CC(C)C#CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 43, 125, 125, 125, 125, 125, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 18, 18, 125, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277902 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277902
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277902/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277902
Building REAL300025277903
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277903'
/scratch/stefan/7808390/working/building/REAL300025277903 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277903

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277903/0 /scratch/stefan/7808390/working/building/REAL300025277903 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/790
`/scratch/stefan/7808390/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CS1)

`REAL300025277903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277903 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 45, 45, 45, 45, 45, 1, 1, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 9, 9, 45, 1, 1, 1, 26, 26] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43])
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: REAL300025277903 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 26, 26, 26, 26, 26, 37, 37, 73, 114, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 2, 2, 2, 7, 26, 26, 26, 26, 26, 26, 73, 73, 201, 26, 26, 26, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 43, 23, 24, 25] set([4, 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])
total number of confs: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277903 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 99, 99, 99, 45, 45, 45, 45, 45, 31, 27, 31, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 201, 99, 45, 45, 45, 45, 45, 45, 27, 27, 1, 45, 45, 45, 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])
total number of confs: 441
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277903 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277903
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277903/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277903
Building REAL300025277904
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277904'
/scratch/stefan/7808390/working/building/REAL300025277904 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277904

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277904/0 /scratch/stefan/7808390/working/building/REAL300025277904 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/791
`/scratch/stefan/7808390/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1(O)CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277904 none O=C(CC1(O)CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 6, 6, 34, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 68, 68, 68, 68, 68, 1, 1, 34, 34, 114, 38, 38, 38, 38, 38, 38, 6, 1, 1, 1, 1, 1, 1, 7, 7, 68, 1, 1, 1] 603
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 339
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277904 none O=C(CC1(O)CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 4, 1, 1, 1, 1, 1, 1, 13, 13, 38, 38, 38, 38, 38, 51, 51, 74, 114, 201, 201, 201, 201, 201, 38, 38, 4, 4, 6, 1, 1, 1, 1, 1, 1, 13, 38, 38, 38, 38, 38, 38, 74, 74, 201, 38, 38, 38] 603
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 534
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277904 none O=C(CC1(O)CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [146, 146, 146, 201, 201, 201, 201, 201, 68, 68, 68, 68, 68, 44, 31, 44, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 603, 201, 201, 201, 201, 201, 201, 146, 68, 68, 68, 68, 68, 68, 31, 31, 1, 68, 68, 68] 603
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])
total number of confs: 1336
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277904 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277904
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277904/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277904
Building REAL300025277905
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277905'
/scratch/stefan/7808390/working/building/REAL300025277905 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277905

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277905/0 /scratch/stefan/7808390/working/building/REAL300025277905 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/792
`/scratch/stefan/7808390/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277905 none CC1=CNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 29, 93, 93, 93, 93, 93, 1, 1, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 15, 15, 93, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
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: REAL300025277905 none CC1=CNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 3, 3, 12, 12, 12, 12, 12, 22, 22, 63, 112, 201, 201, 201, 201, 201, 12, 12, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 63, 63, 201, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 474
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277905 none CC1=CNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 93, 93, 93, 93, 93, 56, 38, 56, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 93, 93, 38, 38, 1, 93, 93, 93] 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])
total number of confs: 589
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277905 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277905
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277905/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277905
Building REAL300025277906
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277906'
/scratch/stefan/7808390/working/building/REAL300025277906 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277906

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277906/0 /scratch/stefan/7808390/working/building/REAL300025277906 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/793
`/scratch/stefan/7808390/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCC1)

`REAL300025277906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277906 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 126, 126, 126, 61, 61, 61, 61, 61, 39, 34, 39, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 126, 61, 61, 61, 61, 61, 61, 34, 34, 1, 61, 61, 61, 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])
total number of confs: 619
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277906 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 18, 61, 61, 61, 61, 61, 1, 1, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 14, 14, 61, 1, 1, 1, 30, 30, 30, 30, 30, 30] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21, 41, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43, 44, 45, 46, 47])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277906 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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.3', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 53, 53, 107, 145, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 1, 2, 2, 2, 10, 30, 30, 30, 30, 30, 30, 107, 107, 201, 30, 30, 30, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 22, 23, 24, 25] set([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: 592
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277906 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277906
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277906/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277906
Building REAL300025277907
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277907'
/scratch/stefan/7808390/working/building/REAL300025277907 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277907

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277907/0 /scratch/stefan/7808390/working/building/REAL300025277907 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/794
`/scratch/stefan/7808390/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C#CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277907 none O=C(C#CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 19, 56, 56, 56, 56, 56, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 1, 1, 1] 61
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39])
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: REAL300025277907 none O=C(C#CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 18, 34, 61, 61, 61, 61, 61, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 61, 4, 4, 4] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277907 none O=C(C#CC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 56, 56, 56, 56, 56, 45, 35, 45, 12, 1, 1, 1, 1, 1, 1, 1, 56, 56, 61, 61, 61, 61, 61, 61, 56, 56, 56, 56, 56, 56, 35, 35, 1, 56, 56, 56] 61
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])
total number of confs: 195
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277907 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277907
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277907/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277907
Building REAL300025277908
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277908'
/scratch/stefan/7808390/working/building/REAL300025277908 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277908

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277908/0 /scratch/stefan/7808390/working/building/REAL300025277908 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/795
`/scratch/stefan/7808390/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C#CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277908 none CC(C)(C)C#CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 79, 50, 79, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 120, 50, 50, 1, 120, 120, 120] 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])
total number of confs: 626
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277908 none CC(C)(C)C#CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 42, 120, 120, 120, 120, 120, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 16, 16, 120, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277908 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277908
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277908/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277908
Building REAL300025277909
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277909'
/scratch/stefan/7808390/working/building/REAL300025277909 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277909

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277909/0 /scratch/stefan/7808390/working/building/REAL300025277909 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/796
`/scratch/stefan/7808390/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1)

`REAL300025277909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277909 none CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1 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', 'C.3', 'C.3', 'N.am', '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, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 1, 1, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1, 1, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277909 none CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1 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', 'C.3', 'C.3', 'N.am', '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, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 3, 8, 8, 8, 20, 20, 20, 20, 20, 31, 31, 53, 94, 201, 201, 201, 201, 201, 20, 20, 1, 2, 2, 2, 3, 3, 8, 20, 20, 20, 20, 20, 20, 53, 53, 201, 20, 20, 20, 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: 508
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277909 none CC1=NN=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1 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', 'C.3', 'C.3', 'N.am', '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, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 112, 112, 112, 38, 38, 38, 38, 38, 21, 19, 21, 9, 1, 1, 1, 1, 1, 1, 1, 38, 38, 201, 201, 201, 201, 201, 201, 112, 38, 38, 38, 38, 38, 38, 19, 19, 1, 38, 38, 38, 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])
total number of confs: 761
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277909 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277909/1 /scratch/stefan/7808390/working/building/REAL300025277909 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/797
`/scratch/stefan/7808390/working/3D/797' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1)

`REAL300025277909.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277909/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277909 none CC1=NC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 38, 38, 38, 38, 38, 1, 1, 45, 45, 45, 45, 45, 21, 21, 6, 1, 1, 1, 1, 1, 1, 4, 4, 38, 1, 1, 1, 45] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
total number of confs: 168
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277909 none CC1=NC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in 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, 15, 15, 15, 45, 45, 45, 45, 45, 56, 56, 76, 114, 201, 201, 201, 201, 201, 45, 45, 1, 1, 2, 2, 2, 6, 6, 15, 45, 45, 45, 45, 45, 45, 76, 76, 201, 45, 45, 45, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 45, 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])
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: REAL300025277909 none CC1=NC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NN1 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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 87, 87, 87, 38, 38, 38, 38, 38, 29, 26, 29, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 201, 201, 201, 201, 201, 165, 165, 87, 38, 38, 38, 38, 38, 38, 26, 26, 1, 38, 38, 38, 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])
total number of confs: 688
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277909 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277909
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277909/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277909/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277909
Building REAL300025277910
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277910'
/scratch/stefan/7808390/working/building/REAL300025277910 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277910

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277910/0 /scratch/stefan/7808390/working/building/REAL300025277910 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/798
`/scratch/stefan/7808390/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=N1)

`REAL300025277910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277910 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 47, 127, 127, 127, 127, 127, 1, 1, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 27, 27, 127, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
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: REAL300025277910 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 35, 35, 99, 141, 201, 201, 201, 201, 201, 13, 13, 1, 1, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 13, 13, 99, 99, 201, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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])
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: REAL300025277910 none CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=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', 'C.3', 'C.3', 'N.am', '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', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 77, 40, 77, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 127, 40, 40, 1, 127, 127, 127] 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])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277910 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277910
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277910/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277910
Building REAL300025277911
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277911'
/scratch/stefan/7808390/working/building/REAL300025277911 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277911

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277911/0 /scratch/stefan/7808390/working/building/REAL300025277911 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/799
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)[C@@H]3C[C@H]3[N+](=O)[O-])C2C1)

`REAL300025277911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277911 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3[N+](=O)[O-])C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 3, 9, 17, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 56, 56, 1, 1, 9, 9, 78, 1, 1, 1, 1, 1, 1, 5, 23, 23, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 40, 41, 10, 11, 12, 13, 14, 15, 26, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39])
total number of confs: 260
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277911 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3[N+](=O)[O-])C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 40, 13, 1, 1, 1, 1, 1, 1, 1, 59, 78, 78, 78, 78, 78, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 78, 78, 40, 40, 1, 78, 78, 78, 78, 78, 78, 117, 201, 201, 78, 78, 78] 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])
total number of confs: 665
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: REAL300025277911 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3[N+](=O)[O-])C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 23, 36, 70, 107, 201, 201, 201, 201, 201, 23, 23, 23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 70, 70, 201, 23, 23, 23, 23, 23, 23, 10, 1, 1, 23, 23, 23] 201
rigid atoms, others: [38, 39, 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, 35, 36, 37, 40, 41, 42])
total number of confs: 508
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277911 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277911
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277911/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277911
Building REAL300025277912
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277912'
/scratch/stefan/7808390/working/building/REAL300025277912 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277912

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277912/0 /scratch/stefan/7808390/working/building/REAL300025277912 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/800
`/scratch/stefan/7808390/working/3D/800' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(C)N=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277912 none CC1=CN(C)N=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 49, 119, 119, 119, 119, 119, 1, 1, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 29, 29, 119, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025277912 none CC1=CN(C)N=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 3, 3, 12, 12, 12, 12, 12, 33, 33, 101, 148, 201, 201, 201, 201, 201, 12, 12, 2, 2, 2, 1, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 101, 101, 201, 12, 12, 12] 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])
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: REAL300025277912 none CC1=CN(C)N=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 119, 119, 119, 119, 119, 75, 43, 75, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 43, 43, 1, 119, 119, 119] 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])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277912 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277912
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277912/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277912
Building REAL300025277913
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277913'
/scratch/stefan/7808390/working/building/REAL300025277913 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277913

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277913/0 /scratch/stefan/7808390/working/building/REAL300025277913 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/801
`/scratch/stefan/7808390/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC(F)C3)C2C1)

`REAL300025277913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277913 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 1, 1, 8, 8, 49, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277913 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 27, 13, 1, 1, 1, 1, 1, 1, 1, 33, 49, 49, 49, 49, 49, 114, 114, 114, 201, 201, 201, 201, 201, 201, 49, 49, 27, 27, 1, 49, 49, 49, 49, 49, 49, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49] 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: 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: REAL300025277913 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 26, 38, 71, 114, 201, 201, 201, 201, 201, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 26, 26, 71, 71, 201, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49])
total number of confs: 510
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277913 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277913
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277913/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277913
Building REAL300025277914
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277914'
/scratch/stefan/7808390/working/building/REAL300025277914 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277914

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277914/0 /scratch/stefan/7808390/working/building/REAL300025277914 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/802
`/scratch/stefan/7808390/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277914 none CN1C=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 56, 56, 56, 56, 56, 1, 1, 28, 28, 28, 28, 28, 28, 25, 25, 6, 1, 1, 1, 1, 1, 1, 5, 5, 56, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277914 none CN1C=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 28, 28, 28, 28, 28, 38, 38, 57, 97, 201, 201, 201, 201, 201, 28, 28, 1, 2, 2, 2, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 28, 57, 57, 201, 28, 28, 28] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277914 none CN1C=CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 127, 127, 127, 56, 56, 56, 56, 56, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 127, 56, 56, 56, 56, 56, 56, 29, 29, 1, 56, 56, 56] 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])
total number of confs: 753
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277914 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277914
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277914/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277914
Building REAL300025277915
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277915'
/scratch/stefan/7808390/working/building/REAL300025277915 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277915

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277915/0 /scratch/stefan/7808390/working/building/REAL300025277915 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/803
`/scratch/stefan/7808390/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025277915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277915 none COCC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 28, 25, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 49, 49, 49, 49, 49, 1, 1, 25, 25, 29, 29, 29, 28, 28, 19, 19, 6, 1, 1, 1, 1, 1, 1, 6, 6, 49, 1, 1, 1, 25, 25, 25, 25] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277915 none COCC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 14, 14, 14, 25, 25, 25, 25, 25, 30, 30, 54, 82, 198, 198, 198, 198, 198, 25, 25, 1, 1, 9, 9, 9, 6, 6, 7, 7, 14, 25, 25, 25, 25, 25, 25, 54, 54, 198, 25, 25, 25, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 25, 26] set([0, 1, 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: 475
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277915 none COCC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 194, 99, 99, 99, 49, 49, 49, 49, 49, 39, 32, 39, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 198, 198, 201, 201, 201, 201, 201, 194, 194, 99, 49, 49, 49, 49, 49, 49, 32, 32, 1, 49, 49, 49, 198, 198, 198, 198] 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, 50])
total number of confs: 800
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277915 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277915
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277915/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277915
Building REAL300025277916
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277916'
/scratch/stefan/7808390/working/building/REAL300025277916 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277916

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277916/0 /scratch/stefan/7808390/working/building/REAL300025277916 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/804
`/scratch/stefan/7808390/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)NCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277916 none NC(=O)NCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 180, 76, 76, 76, 32, 32, 32, 32, 32, 24, 21, 24, 10, 1, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 201, 201, 180, 180, 76, 32, 32, 32, 32, 32, 32, 21, 21, 1, 32, 32, 32] 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])
total number of confs: 783
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277916 none NC(=O)NCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [42, 42, 42, 41, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 32, 32, 32, 32, 32, 1, 1, 42, 42, 42, 41, 41, 30, 30, 5, 1, 1, 1, 1, 1, 1, 4, 4, 32, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277916 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277916
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277916/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277916
Building REAL300025277917
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277917'
/scratch/stefan/7808390/working/building/REAL300025277917 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277917

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277917/0 /scratch/stefan/7808390/working/building/REAL300025277917 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/805
`/scratch/stefan/7808390/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277917 none CC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 20, 58, 58, 58, 58, 58, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 15, 15, 58, 1, 1, 1, 30, 30] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 24, 39, 47, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 48, 49])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277917 none CC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 30, 30, 30, 30, 30, 51, 51, 107, 144, 201, 201, 201, 201, 201, 30, 30, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 30, 107, 107, 201, 30, 30, 30, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 48, 49, 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])
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: REAL300025277917 none CC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 111, 111, 111, 58, 58, 58, 58, 58, 38, 33, 38, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 58, 58, 58, 58, 58, 58, 33, 33, 1, 58, 58, 58, 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])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277917 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277917
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277917/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277917
Building REAL300025277918
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277918'
/scratch/stefan/7808390/working/building/REAL300025277918 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277918

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277918/0 /scratch/stefan/7808390/working/building/REAL300025277918 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/806
`/scratch/stefan/7808390/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277918 none CCN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 79, 79, 79, 79, 79, 1, 1, 10, 24, 24, 24, 24, 24, 10, 10, 6, 1, 1, 1, 1, 1, 1, 7, 7, 79, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277918 none CCN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 3, 3, 10, 10, 10, 10, 10, 16, 16, 34, 64, 164, 164, 164, 164, 164, 10, 10, 1, 7, 7, 7, 7, 7, 1, 1, 3, 10, 10, 10, 10, 10, 10, 34, 34, 164, 10, 10, 10] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 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: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277918 none CCN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 162, 162, 162, 79, 79, 79, 79, 79, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 164, 201, 201, 201, 201, 201, 164, 164, 162, 79, 79, 79, 79, 79, 79, 30, 30, 1, 79, 79, 79] 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277918 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277918
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277918/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277918
Building REAL300025277919
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277919'
/scratch/stefan/7808390/working/building/REAL300025277919 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277919

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277919/0 /scratch/stefan/7808390/working/building/REAL300025277919 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/807
`/scratch/stefan/7808390/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)C)

`REAL300025277919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277919 none CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [189, 189, 189, 157, 157, 157, 60, 60, 60, 60, 60, 39, 32, 39, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 189, 201, 201, 189, 189, 189, 189, 189, 189, 157, 60, 60, 60, 60, 60, 60, 32, 32, 1, 60, 60, 60, 201, 201, 201, 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, 51, 52])
total number of confs: 721
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277919 none CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 60, 60, 60, 60, 60, 1, 1, 11, 21, 21, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 6, 6, 60, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277919 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277919
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277919/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277919
Building REAL300025277920
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277920'
/scratch/stefan/7808390/working/building/REAL300025277920 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277920

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277920/0 /scratch/stefan/7808390/working/building/REAL300025277920 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/808
`/scratch/stefan/7808390/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277920 none C#CCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 122, 122, 122, 68, 68, 68, 20, 20, 20, 20, 20, 14, 13, 14, 9, 1, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 122, 122, 122, 122, 68, 20, 20, 20, 20, 20, 20, 13, 13, 1, 20, 20, 20] 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])
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: REAL300025277920 none C#CCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 20, 20, 20, 20, 20, 1, 1, 24, 24, 24, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 5, 5, 20, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277920 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277920
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277920/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277920
Building REAL300025277921
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277921'
/scratch/stefan/7808390/working/building/REAL300025277921 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277921

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277921/0 /scratch/stefan/7808390/working/building/REAL300025277921 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/809
`/scratch/stefan/7808390/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277921 none C#CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 160, 160, 138, 160, 138, 138, 58, 58, 58, 58, 58, 39, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 160, 160, 160, 160, 138, 58, 58, 58, 58, 58, 58, 33, 33, 1, 58, 58, 58] 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])
total number of confs: 783
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277921 none C#CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [27, 27, 13, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 58, 58, 58, 58, 58, 1, 1, 27, 27, 27, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 6, 6, 58, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277921 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277921
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277921/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277921
Building REAL300025277922
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277922'
/scratch/stefan/7808390/working/building/REAL300025277922 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277922

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277922/0 /scratch/stefan/7808390/working/building/REAL300025277922 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/810
`/scratch/stefan/7808390/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277922 none O=C(CCOCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 13, 16, 24, 24, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 1, 1, 11, 11, 11, 11, 16, 16, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277922 none O=C(CCOCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 10, 8, 6, 3, 1, 1, 1, 1, 11, 11, 24, 24, 24, 24, 24, 32, 32, 55, 98, 201, 201, 201, 201, 201, 24, 24, 10, 10, 8, 8, 3, 3, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 24, 24, 55, 55, 201, 24, 24, 24] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 37] 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, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277922 none O=C(CCOCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 171, 171, 173, 174, 201, 201, 38, 38, 38, 38, 38, 26, 23, 26, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 171, 171, 171, 171, 174, 174, 201, 201, 201, 201, 201, 108, 38, 38, 38, 38, 38, 38, 23, 23, 1, 38, 38, 38] 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])
total number of confs: 789
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277922 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277922
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277922/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277922
Building REAL300025277923
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277923'
/scratch/stefan/7808390/working/building/REAL300025277923 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277923

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277923/0 /scratch/stefan/7808390/working/building/REAL300025277923 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/811
`/scratch/stefan/7808390/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277923 none O=C(COC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 32, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 48, 48, 48, 48, 48, 1, 1, 23, 23, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 1, 1, 6, 6, 48, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277923 none O=C(COC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 15, 15, 37, 37, 37, 37, 37, 48, 48, 77, 106, 201, 201, 201, 201, 201, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 15, 37, 37, 37, 37, 37, 37, 77, 77, 201, 37, 37, 37] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 535
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277923 none O=C(COC1CCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 186, 192, 201, 201, 201, 201, 48, 48, 48, 48, 48, 37, 31, 37, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 186, 186, 201, 201, 201, 201, 201, 201, 201, 103, 48, 48, 48, 48, 48, 48, 31, 31, 1, 48, 48, 48] 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])
total number of confs: 761
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277923 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277923
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277923/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277923
Building REAL300025277924
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277924'
/scratch/stefan/7808390/working/building/REAL300025277924 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277924

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277924/0 /scratch/stefan/7808390/working/building/REAL300025277924 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/812
`/scratch/stefan/7808390/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)NC(N)=O)

`REAL300025277924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277924 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)NC(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'N.am', '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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 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: [200, 201, 131, 131, 131, 62, 62, 62, 62, 62, 41, 34, 41, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 62, 62, 62, 62, 62, 62, 34, 34, 1, 62, 62, 62, 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])
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: REAL300025277924 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)NC(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'N.am', '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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 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: [29, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 62, 62, 62, 62, 62, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 25, 25, 6, 1, 1, 1, 1, 1, 1, 6, 6, 62, 1, 1, 1, 34, 34, 34] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 45, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277924 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277924
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277924/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277924
Building REAL300025277925
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277925'
/scratch/stefan/7808390/working/building/REAL300025277925 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277925

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277925/0 /scratch/stefan/7808390/working/building/REAL300025277925 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/813
`/scratch/stefan/7808390/working/3D/813' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C(F)F)CC3)C2C1)

`REAL300025277925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277925 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C(F)F)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 10, 16, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 37, 37, 15, 15, 1, 1, 10, 10, 65, 1, 1, 1, 1, 1, 1, 5, 37, 15, 15, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 232
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277925 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C(F)F)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 34, 13, 1, 1, 1, 1, 1, 1, 1, 47, 65, 65, 65, 65, 65, 102, 102, 102, 182, 201, 201, 182, 182, 65, 65, 34, 34, 1, 65, 65, 65, 65, 65, 65, 102, 201, 182, 182, 182, 182, 65, 65, 65] 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: 678
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277925 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C(F)F)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 15, 26, 45, 72, 181, 181, 181, 181, 181, 15, 15, 15, 15, 7, 7, 1, 7, 1, 1, 8, 8, 1, 1, 15, 15, 45, 45, 181, 15, 15, 15, 15, 15, 15, 7, 8, 1, 1, 1, 1, 15, 15, 15] 201
rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 429
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277925 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277925
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277925/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277925
Building REAL300025277926
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277926'
/scratch/stefan/7808390/working/building/REAL300025277926 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277926

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277926/0 /scratch/stefan/7808390/working/building/REAL300025277926 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/814
`/scratch/stefan/7808390/working/3D/814' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277926 none C=CCC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 172, 90, 172, 172, 90, 90, 45, 45, 45, 45, 45, 32, 29, 32, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 172, 172, 172, 172, 172, 172, 90, 45, 45, 45, 45, 45, 45, 29, 29, 1, 45, 45, 45] 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])
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: REAL300025277926 none C=CCC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 45, 45, 45, 45, 45, 1, 1, 37, 37, 37, 25, 25, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277926 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277926
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277926/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277926
Building REAL300025277927
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277927'
/scratch/stefan/7808390/working/building/REAL300025277927 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277927

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277927/0 /scratch/stefan/7808390/working/building/REAL300025277927 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/815
`/scratch/stefan/7808390/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC34CCC4)C2C1)

`REAL300025277927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277927 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC34CCC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 13, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 1, 1, 8, 8, 64, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025277927 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC34CCC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 48, 64, 64, 64, 64, 64, 126, 126, 126, 201, 201, 201, 201, 201, 64, 64, 42, 42, 1, 64, 64, 64, 64, 64, 64, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64] 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: 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: REAL300025277927 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC34CCC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 35, 68, 108, 201, 201, 201, 201, 201, 28, 28, 28, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 28, 68, 68, 201, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 35, 45, 46, 47])
total number of confs: 505
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277927 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277927
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277927/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277927
Building REAL300025277928
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277928'
/scratch/stefan/7808390/working/building/REAL300025277928 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277928

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277928/0 /scratch/stefan/7808390/working/building/REAL300025277928 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/816
`/scratch/stefan/7808390/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277928 none CC1=CC=NN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 25, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 53, 53, 53, 53, 53, 1, 1, 25, 25, 25, 25, 25, 23, 23, 6, 1, 1, 1, 1, 1, 1, 5, 5, 53, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025277928 none CC1=CC=NN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 9, 9, 9, 25, 25, 25, 25, 25, 37, 37, 64, 104, 201, 201, 201, 201, 201, 25, 25, 2, 2, 2, 1, 1, 4, 4, 9, 25, 25, 25, 25, 25, 25, 64, 64, 201, 25, 25, 25] 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: 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: REAL300025277928 none CC1=CC=NN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 137, 137, 137, 53, 53, 53, 53, 53, 34, 28, 34, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 201, 201, 137, 53, 53, 53, 53, 53, 53, 28, 28, 1, 53, 53, 53] 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])
total number of confs: 755
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277928 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277928
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277928/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277928
Building REAL300025277929
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277929'
/scratch/stefan/7808390/working/building/REAL300025277929 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277929

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277929/0 /scratch/stefan/7808390/working/building/REAL300025277929 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/817
`/scratch/stefan/7808390/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=NO1)

`REAL300025277929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277929 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [33, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 64, 64, 64, 64, 64, 1, 1, 18, 18, 18, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 8, 8, 64, 1, 1, 1, 18] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277929 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 25, 25, 44, 69, 181, 181, 181, 181, 181, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 6, 18, 18, 18, 18, 18, 18, 44, 44, 181, 18, 18, 18, 1] 201
rigid atoms, others: [1, 2, 3, 4, 45, 24, 25, 26] set([0, 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])
total number of confs: 401
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277929 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 181, 181, 150, 150, 150, 64, 64, 64, 64, 64, 41, 31, 41, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 181, 181, 181, 201, 201, 201, 201, 201, 150, 64, 64, 64, 64, 64, 64, 31, 31, 1, 64, 64, 64, 181] 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: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277929 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277929
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277929/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277929
Building REAL300025277930
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277930'
/scratch/stefan/7808390/working/building/REAL300025277930 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277930

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277930/0 /scratch/stefan/7808390/working/building/REAL300025277930 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/818
`/scratch/stefan/7808390/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CSC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277930 none O=C(CC1=CSC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 14, 1, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 29, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 87, 87, 87, 87, 87, 1, 1, 29, 29, 40, 40, 6, 1, 1, 1, 1, 1, 1, 13, 13, 87, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 252
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: REAL300025277930 none O=C(CC1=CSC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 14, 1, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 22, 22, 40, 40, 40, 40, 40, 53, 53, 80, 108, 201, 201, 201, 201, 201, 40, 40, 4, 4, 1, 1, 22, 40, 40, 40, 40, 40, 40, 80, 80, 201, 40, 40, 40] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29] set([0, 1, 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: 517
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: REAL300025277930 none O=C(CC1=CSC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 14, 1, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 197, 201, 201, 201, 201, 87, 87, 87, 87, 87, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 197, 197, 201, 201, 135, 87, 87, 87, 87, 87, 87, 30, 30, 1, 87, 87, 87] 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])
total number of confs: 729
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277930 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277930
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277930/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277930
Building REAL300025277931
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277931'
/scratch/stefan/7808390/working/building/REAL300025277931 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277931

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277931/0 /scratch/stefan/7808390/working/building/REAL300025277931 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/819
`/scratch/stefan/7808390/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277931 none CN(C)C(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 201, 108, 108, 108, 46, 46, 46, 46, 46, 31, 25, 31, 12, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 201, 201, 201, 172, 172, 108, 46, 46, 46, 46, 46, 46, 25, 25, 1, 46, 46, 46] 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])
total number of confs: 753
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: REAL300025277931 none CN(C)C(=O)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 46, 21, 44, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 1, 46, 46, 46, 46, 46, 46, 21, 21, 5, 1, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 229
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277931 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277931
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277931/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277931
Building REAL300025277932
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277932'
/scratch/stefan/7808390/working/building/REAL300025277932 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277932

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277932/0 /scratch/stefan/7808390/working/building/REAL300025277932 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/820
`/scratch/stefan/7808390/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277932 none CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 126, 126, 126, 126, 126, 1, 1, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 27, 27, 126, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
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: REAL300025277932 none CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 3, 13, 13, 13, 13, 13, 33, 33, 101, 143, 201, 201, 201, 201, 201, 13, 13, 1, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 101, 101, 201, 13, 13, 13] 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])
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: REAL300025277932 none CN1C=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 126, 126, 126, 126, 126, 82, 43, 82, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 126, 43, 43, 1, 126, 126, 126] 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])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277932 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277932
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277932/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277932
Building REAL300025277933
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277933'
/scratch/stefan/7808390/working/building/REAL300025277933 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277933

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277933/0 /scratch/stefan/7808390/working/building/REAL300025277933 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/821
`/scratch/stefan/7808390/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277933 none CC1=NC=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 43, 43, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 60, 60, 60, 60, 60, 1, 1, 43, 43, 43, 43, 43, 23, 23, 4, 1, 1, 1, 1, 1, 1, 7, 7, 60, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277933 none CC1=NC=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 28, 28, 28, 43, 43, 43, 43, 43, 53, 53, 87, 120, 201, 201, 201, 201, 201, 43, 43, 2, 2, 2, 1, 1, 7, 7, 28, 43, 43, 43, 43, 43, 43, 87, 87, 201, 43, 43, 43] 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: 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: REAL300025277933 none CC1=NC=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 184, 102, 102, 102, 60, 60, 60, 60, 60, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 184, 184, 102, 60, 60, 60, 60, 60, 60, 30, 30, 1, 60, 60, 60] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277933 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277933/1 /scratch/stefan/7808390/working/building/REAL300025277933 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/822
`/scratch/stefan/7808390/working/3D/822' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=[NH+]C=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277933.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277933/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277933 none CC1=[NH+]C=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 55, 55, 55, 55, 55, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 37, 37, 37, 37, 37, 1, 1, 55, 55, 55, 55, 55, 29, 29, 6, 1, 1, 1, 1, 1, 1, 6, 6, 37, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 47, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 204
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277933 none CC1=[NH+]C=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 17, 17, 17, 55, 55, 55, 55, 55, 77, 77, 121, 130, 201, 201, 201, 201, 201, 55, 55, 2, 2, 2, 1, 1, 5, 5, 17, 55, 55, 55, 55, 55, 55, 121, 121, 201, 55, 55, 55] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 641
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277933 none CC1=[NH+]C=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 166, 91, 91, 91, 37, 37, 37, 37, 37, 25, 23, 25, 11, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 166, 166, 91, 37, 37, 37, 37, 37, 37, 23, 23, 1, 37, 37, 37] 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])
total number of confs: 704
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277933 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277933
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277933/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277933/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277933
Building REAL300025277934
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277934'
/scratch/stefan/7808390/working/building/REAL300025277934 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277934

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277934/0 /scratch/stefan/7808390/working/building/REAL300025277934 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/823
`/scratch/stefan/7808390/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277934 none CCN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 14, 55, 55, 55, 55, 55, 1, 1, 23, 23, 23, 23, 23, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 9, 9, 55, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 172
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: REAL300025277934 none CCN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 13, 13, 13, 13, 13, 24, 24, 44, 71, 138, 138, 138, 138, 138, 13, 13, 3, 3, 3, 3, 3, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 44, 44, 138, 13, 13, 13] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34] set([0, 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, 46, 47])
total number of confs: 365
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: REAL300025277934 none CCN1C=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 138, 138, 138, 138, 138, 104, 104, 104, 55, 55, 55, 55, 55, 40, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 138, 138, 138, 104, 55, 55, 55, 55, 55, 55, 29, 29, 1, 55, 55, 55] 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])
total number of confs: 767
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277934 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277934
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277934/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277934
Building REAL300025277935
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277935'
/scratch/stefan/7808390/working/building/REAL300025277935 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277935

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277935/0 /scratch/stefan/7808390/working/building/REAL300025277935 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/824
`/scratch/stefan/7808390/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277935 none O=C(CC1CCCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 54, 54, 54, 54, 54, 1, 1, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 1, 1, 1, 1, 1, 1, 8, 8, 54, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
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: REAL300025277935 none O=C(CC1CCCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 28, 28, 47, 47, 47, 47, 47, 61, 61, 88, 122, 201, 201, 201, 201, 201, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 47, 47, 47, 47, 47, 47, 88, 88, 201, 47, 47, 47] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 555
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277935 none O=C(CC1CCCOC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 189, 201, 201, 201, 201, 201, 54, 54, 54, 54, 54, 46, 26, 46, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 54, 54, 54, 54, 54, 54, 26, 26, 1, 54, 54, 54] 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])
total number of confs: 780
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277935 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277935
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277935/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277935
Building REAL300025277936
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277936'
/scratch/stefan/7808390/working/building/REAL300025277936 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277936

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277936/0 /scratch/stefan/7808390/working/building/REAL300025277936 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/825
`/scratch/stefan/7808390/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC=CCC3)C2C1)

`REAL300025277936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277936 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC=CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 16, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 1, 1, 9, 9, 57, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 158
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277936 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC=CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 12, 1, 1, 1, 1, 1, 1, 1, 39, 57, 57, 57, 57, 57, 120, 120, 120, 201, 201, 201, 201, 201, 201, 57, 57, 32, 32, 1, 57, 57, 57, 57, 57, 57, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 57, 57, 57] 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: 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: REAL300025277936 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC=CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 36, 72, 108, 201, 201, 201, 201, 201, 26, 26, 26, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 72, 72, 201, 26, 26, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 504
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277936 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277936
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277936/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277936
Building REAL300025277937
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277937'
/scratch/stefan/7808390/working/building/REAL300025277937 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277937

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277937/0 /scratch/stefan/7808390/working/building/REAL300025277937 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/826
`/scratch/stefan/7808390/working/3D/826' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025277937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277937 none CC1=NC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 48, 116, 116, 116, 116, 116, 1, 1, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 27, 27, 116, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277937 none CC1=NC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 1, 4, 4, 4, 15, 15, 15, 15, 15, 37, 37, 108, 153, 201, 201, 201, 201, 201, 15, 15, 1, 2, 2, 2, 1, 1, 4, 15, 15, 15, 15, 15, 15, 108, 108, 201, 15, 15, 15] 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])
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: REAL300025277937 none CC1=NC=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 200, 200, 200, 116, 116, 116, 116, 116, 75, 42, 75, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 200, 116, 116, 116, 116, 116, 116, 42, 42, 1, 116, 116, 116] 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])
total number of confs: 648
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277937 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277937
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277937/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277937
Building REAL300025277938
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277938'
/scratch/stefan/7808390/working/building/REAL300025277938 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277938

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277938/0 /scratch/stefan/7808390/working/building/REAL300025277938 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/827
`/scratch/stefan/7808390/working/3D/827' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277938 none COCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 115, 201, 115, 115, 51, 51, 51, 51, 51, 35, 29, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 51, 51, 51, 51, 51, 51, 29, 29, 1, 51, 51, 51] 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])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277938 none COCCC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 6, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 51, 51, 51, 51, 51, 1, 1, 25, 25, 25, 25, 25, 25, 25, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277938 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277938
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277938/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277938
Building REAL300025277939
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277939'
/scratch/stefan/7808390/working/building/REAL300025277939 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277939

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277939/0 /scratch/stefan/7808390/working/building/REAL300025277939 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/828
`/scratch/stefan/7808390/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277939 none CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 170, 169, 112, 112, 112, 64, 64, 64, 64, 64, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 169, 201, 201, 170, 170, 170, 170, 170, 169, 112, 64, 64, 64, 64, 64, 64, 35, 35, 1, 64, 64, 64, 201, 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: 800
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: REAL300025277939 none CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 64, 64, 64, 64, 64, 1, 1, 13, 25, 25, 15, 15, 15, 15, 15, 13, 6, 1, 1, 1, 1, 1, 1, 7, 7, 64, 1, 1, 1, 25, 25, 25, 25, 25] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50])
total number of confs: 180
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: REAL300025277939 none CCOC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 6, 11, 11, 11, 25, 25, 25, 25, 25, 37, 37, 62, 92, 201, 201, 201, 201, 201, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 25, 25, 25, 25, 25, 25, 62, 62, 201, 25, 25, 25, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 46, 47, 48, 49, 50, 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, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 493
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277939 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277939
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277939/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277939
Building REAL300025277940
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277940'
/scratch/stefan/7808390/working/building/REAL300025277940 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277940

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277940/0 /scratch/stefan/7808390/working/building/REAL300025277940 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/829
`/scratch/stefan/7808390/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1N=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277940 none O=C(CN1N=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 8, 1, 8, 8, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 17, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 73, 73, 73, 73, 73, 1, 1, 17, 17, 43, 4, 1, 1, 1, 1, 1, 1, 10, 10, 73, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 36, 37, 38])
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: REAL300025277940 none O=C(CN1N=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 8, 1, 8, 8, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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: [33, 9, 1, 1, 1, 1, 1, 1, 33, 33, 43, 43, 43, 43, 43, 57, 57, 83, 118, 201, 201, 201, 201, 201, 43, 43, 9, 9, 1, 33, 43, 43, 43, 43, 43, 43, 83, 83, 201, 43, 43, 43] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28] set([0, 1, 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: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277940 none O=C(CN1N=CN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 8, 1, 8, 8, 8, 5, 5, 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, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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: [113, 113, 113, 177, 201, 201, 201, 201, 73, 73, 73, 73, 73, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 177, 177, 201, 113, 73, 73, 73, 73, 73, 73, 31, 31, 1, 73, 73, 73] 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])
total number of confs: 733
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277940 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277940
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277940/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277940
Building REAL300025277941
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277941'
/scratch/stefan/7808390/working/building/REAL300025277941 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277941

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277941/0 /scratch/stefan/7808390/working/building/REAL300025277941 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/830
`/scratch/stefan/7808390/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC[C@@H](C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277941 none CCCC[C@@H](C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 171, 75, 171, 171, 75, 75, 25, 25, 25, 25, 25, 19, 16, 19, 10, 1, 1, 1, 1, 1, 1, 1, 25, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 75, 25, 25, 25, 25, 25, 25, 16, 16, 1, 25, 25, 25] 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])
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: REAL300025277941 none CCCC[C@@H](C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 6, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 7, 25, 25, 25, 25, 25, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 4, 4, 25, 1, 1, 1] 201
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 49, 50, 51, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277941 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277941
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277941/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277941
Building REAL300025277942
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277942'
/scratch/stefan/7808390/working/building/REAL300025277942 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277942

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277942/0 /scratch/stefan/7808390/working/building/REAL300025277942 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/831
`/scratch/stefan/7808390/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(CC=C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277942 none C=CCC(CC=C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [181, 158, 144, 75, 144, 166, 192, 75, 75, 33, 33, 33, 33, 33, 24, 21, 24, 11, 1, 1, 1, 1, 1, 1, 1, 33, 33, 181, 181, 181, 158, 158, 144, 166, 166, 192, 192, 192, 75, 33, 33, 33, 33, 33, 33, 21, 21, 1, 33, 33, 33] 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])
total number of confs: 1003
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277942 none C=CCC(CC=C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 18, 12, 5, 12, 17, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 33, 33, 33, 33, 33, 1, 1, 26, 26, 26, 18, 18, 12, 17, 17, 24, 24, 24, 5, 1, 1, 1, 1, 1, 1, 6, 6, 33, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277942 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277942
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277942/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277942
Building REAL300025277943
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277943'
/scratch/stefan/7808390/working/building/REAL300025277943 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277943

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277943/0 /scratch/stefan/7808390/working/building/REAL300025277943 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/832
`/scratch/stefan/7808390/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC=CCC1)

`REAL300025277943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277943 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 23, 75, 75, 75, 75, 75, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277943 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 27, 27, 67, 108, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 1, 1, 2, 2, 2, 6, 12, 12, 12, 12, 12, 12, 67, 67, 201, 12, 12, 12, 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: 505
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: REAL300025277943 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 99, 99, 99, 75, 75, 75, 75, 75, 57, 45, 57, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 201, 201, 201, 99, 75, 75, 75, 75, 75, 75, 45, 45, 1, 75, 75, 75, 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])
total number of confs: 640
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277943 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277943
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277943/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277943
Building REAL300025277944
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277944'
/scratch/stefan/7808390/working/building/REAL300025277944 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277944

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277944/0 /scratch/stefan/7808390/working/building/REAL300025277944 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/833
`/scratch/stefan/7808390/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277944 none CCC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 120, 201, 201, 69, 69, 69, 30, 30, 30, 30, 30, 22, 20, 22, 10, 1, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 69, 30, 30, 30, 30, 30, 30, 20, 20, 1, 30, 30, 30] 201
rigid atoms, others: [48, 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, 49, 50, 51])
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: REAL300025277944 none CCC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 44, 18, 44, 44, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 30, 30, 30, 30, 30, 1, 1, 61, 61, 61, 61, 61, 44, 44, 44, 44, 44, 44, 18, 18, 6, 1, 1, 1, 1, 1, 1, 4, 4, 30, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 310
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277944 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277944
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277944/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277944
Building REAL300025277945
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277945'
/scratch/stefan/7808390/working/building/REAL300025277945 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277945

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277945/0 /scratch/stefan/7808390/working/building/REAL300025277945 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/834
`/scratch/stefan/7808390/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277945 none CC(C)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 105, 201, 201, 105, 105, 61, 61, 61, 61, 61, 42, 26, 42, 12, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 61, 61, 61, 61, 61, 61, 26, 26, 1, 61, 61, 61] 201
rigid atoms, others: [48, 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, 49, 50, 51])
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: REAL300025277945 none CC(C)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 16, 61, 61, 61, 61, 61, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 7, 7, 61, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277945 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277945
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277945/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277945
Building REAL300025277946
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277946'
/scratch/stefan/7808390/working/building/REAL300025277946 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277946

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277946/0 /scratch/stefan/7808390/working/building/REAL300025277946 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/835
`/scratch/stefan/7808390/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(Cl)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277946 none C=C(Cl)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 123, 196, 196, 123, 123, 72, 72, 72, 72, 72, 46, 36, 46, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 196, 196, 196, 196, 196, 196, 123, 72, 72, 72, 72, 72, 72, 36, 36, 1, 72, 72, 72] 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])
total number of confs: 858
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277946 none C=C(Cl)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 6, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 72, 72, 72, 72, 72, 1, 1, 26, 26, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 6, 6, 72, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277946 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277946
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277946/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277946
Building REAL300025277947
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277947'
/scratch/stefan/7808390/working/building/REAL300025277947 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277947

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277947/0 /scratch/stefan/7808390/working/building/REAL300025277947 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/836
`/scratch/stefan/7808390/working/3D/836' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277947 none C=CC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 152, 201, 201, 96, 96, 96, 52, 52, 52, 52, 52, 39, 34, 39, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 96, 52, 52, 52, 52, 52, 52, 34, 34, 1, 52, 52, 52] 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])
total number of confs: 918
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277947 none C=CC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 21, 11, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 52, 52, 52, 52, 52, 1, 1, 31, 31, 31, 21, 21, 21, 21, 21, 21, 11, 11, 6, 1, 1, 1, 1, 1, 1, 6, 6, 52, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277947 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277947
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277947/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277947
Building REAL300025277948
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277948'
/scratch/stefan/7808390/working/building/REAL300025277948 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277948

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277948/0 /scratch/stefan/7808390/working/building/REAL300025277948 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/837
`/scratch/stefan/7808390/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1N=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277948 none O=C(CN1N=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 26, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 59, 59, 59, 59, 59, 1, 1, 26, 26, 38, 38, 6, 1, 1, 1, 1, 1, 1, 5, 5, 59, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277948 none O=C(CN1N=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [14, 4, 1, 1, 1, 1, 1, 1, 14, 14, 35, 35, 35, 35, 35, 49, 49, 75, 110, 201, 201, 201, 201, 201, 35, 35, 4, 4, 1, 1, 14, 35, 35, 35, 35, 35, 35, 75, 75, 201, 35, 35, 35] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29] set([0, 1, 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: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277948 none O=C(CN1N=CC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 1, 1, 8, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [136, 136, 136, 201, 201, 201, 201, 201, 59, 59, 59, 59, 59, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 136, 59, 59, 59, 59, 59, 59, 29, 29, 1, 59, 59, 59] 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])
total number of confs: 763
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277948 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277948
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277948/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277948
Building REAL300025277949
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277949'
/scratch/stefan/7808390/working/building/REAL300025277949 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277949

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277949/0 /scratch/stefan/7808390/working/building/REAL300025277949 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/838
`/scratch/stefan/7808390/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277949 none O=C(CCC1=CNN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 33, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 40, 40, 40, 40, 40, 1, 1, 33, 33, 43, 43, 43, 43, 43, 6, 1, 1, 1, 1, 1, 1, 5, 5, 40, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025277949 none O=C(CCC1=CNN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 4, 2, 1, 1, 1, 1, 1, 1, 17, 17, 44, 44, 44, 44, 44, 52, 52, 75, 117, 201, 201, 201, 201, 201, 44, 44, 4, 4, 2, 2, 1, 1, 1, 17, 44, 44, 44, 44, 44, 44, 75, 75, 201, 44, 44, 44] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025277949 none O=C(CCC1=CNN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [102, 102, 102, 190, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 28, 24, 28, 12, 1, 1, 1, 1, 1, 1, 1, 40, 40, 190, 190, 201, 201, 201, 201, 201, 102, 40, 40, 40, 40, 40, 40, 24, 24, 1, 40, 40, 40] 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])
total number of confs: 769
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277949 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277949
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277949/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277949
Building REAL300025277950
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277950'
/scratch/stefan/7808390/working/building/REAL300025277950 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277950

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277950/0 /scratch/stefan/7808390/working/building/REAL300025277950 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/839
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CC3)C2C1)

`REAL300025277950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277950 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 8, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 4, 4, 4, 27, 27, 27, 27, 27, 61, 61, 1, 1, 5, 5, 50, 1, 1, 1, 1, 1, 1, 4, 27, 27, 61, 61, 61, 61, 61, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 47, 10, 11, 12, 13, 14, 15, 46, 45, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 239
number of broken/clashed sets: 1
./output.2.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: REAL300025277950 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 81, 105, 139, 201, 201, 201, 201, 201, 61, 61, 61, 61, 33, 33, 5, 33, 5, 5, 5, 1, 5, 1, 1, 1, 61, 61, 105, 105, 201, 61, 61, 61, 61, 61, 61, 33, 5, 5, 1, 1, 1, 1, 1, 61, 61, 61] 201
rigid atoms, others: [40, 41, 42, 43, 44, 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, 45, 46, 47])
total number of confs: 581
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277950 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 84, 84, 84, 198, 198, 198, 198, 198, 201, 201, 50, 50, 32, 32, 1, 50, 50, 50, 50, 50, 50, 84, 198, 198, 201, 201, 201, 201, 201, 50, 50, 50] 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: 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: REAL300025277950 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 41, 60, 87, 198, 198, 198, 198, 198, 27, 27, 27, 27, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 27, 27, 60, 60, 198, 27, 27, 27, 27, 27, 27, 11, 1, 1, 5, 5, 5, 5, 5, 27, 27, 27] 201
rigid atoms, others: [38, 39, 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, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 475
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277950 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277950
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277950/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277950
Building REAL300025277951
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277951'
/scratch/stefan/7808390/working/building/REAL300025277951 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277951

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277951/0 /scratch/stefan/7808390/working/building/REAL300025277951 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/840
`/scratch/stefan/7808390/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CCC3)C2C1)

`REAL300025277951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277951 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 12, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 4, 4, 4, 29, 29, 29, 29, 29, 45, 45, 45, 1, 1, 7, 7, 56, 1, 1, 1, 1, 1, 1, 4, 29, 29, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300025277951 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 58, 89, 121, 201, 201, 201, 201, 201, 45, 45, 45, 45, 25, 25, 5, 25, 5, 5, 5, 1, 5, 1, 1, 1, 1, 45, 45, 89, 89, 201, 45, 45, 45, 45, 45, 45, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 21, 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, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50])
total number of confs: 544
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277951 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 56, 56, 56, 56, 99, 99, 99, 187, 187, 187, 187, 187, 201, 201, 201, 56, 56, 29, 29, 1, 56, 56, 56, 56, 56, 56, 99, 187, 187, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56] 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, 48, 49, 50])
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: REAL300025277951 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3C[C@H]3C3CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 42, 73, 103, 187, 187, 187, 187, 187, 29, 29, 29, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 29, 73, 73, 187, 29, 29, 29, 29, 29, 29, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29] 201
rigid atoms, others: [39, 40, 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, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 502
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277951 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277951
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277951/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277951
Building REAL300025277952
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277952'
/scratch/stefan/7808390/working/building/REAL300025277952 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277952

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277952/0 /scratch/stefan/7808390/working/building/REAL300025277952 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/841
`/scratch/stefan/7808390/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC[N@@H+]1C)

`REAL300025277952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277952 none C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 4
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277952 none C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
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, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2] 4
rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 48, 49, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277952 none C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4
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, 50, 51, 52])
total number of confs: 10
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277952 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277952/1 /scratch/stefan/7808390/working/building/REAL300025277952 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/842
`/scratch/stefan/7808390/working/3D/842' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC[N@H+]1C)

`REAL300025277952.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277952/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277952 none C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 6, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 22, 55, 55, 55, 55, 55, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 17, 17, 55, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 91
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 136
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277952 none C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 24, 24, 47, 59, 91, 91, 91, 91, 91, 8, 8, 1, 1, 1, 1, 1, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 47, 47, 91, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2] 91
rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 48, 49, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52])
total number of confs: 264
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277952 none C[C@@H]1[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 55, 55, 55, 55, 55, 42, 36, 42, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 91, 91, 91, 91, 91, 91, 91, 91, 91, 55, 55, 55, 55, 55, 55, 36, 36, 1, 55, 55, 55, 91, 91, 91, 91, 91, 91, 91] 91
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, 50, 51, 52])
total number of confs: 291
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277952 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277952
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277952/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277952/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277952
Building REAL300025277953
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277953'
/scratch/stefan/7808390/working/building/REAL300025277953 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277953

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277953/0 /scratch/stefan/7808390/working/building/REAL300025277953 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/843
`/scratch/stefan/7808390/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277953 none CCC(C)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 197, 160, 197, 197, 197, 160, 160, 89, 89, 89, 89, 89, 57, 41, 57, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 197, 197, 197, 201, 201, 201, 201, 201, 160, 89, 89, 89, 89, 89, 89, 41, 41, 1, 89, 89, 89] 201
rigid atoms, others: [48, 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, 49, 50, 51])
total number of confs: 778
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277953 none CCC(C)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 6, 17, 17, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 89, 89, 89, 89, 89, 1, 1, 22, 22, 22, 22, 22, 17, 17, 17, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 9, 9, 89, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277953 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277953
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277953/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277953
Building REAL300025277954
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277954'
/scratch/stefan/7808390/working/building/REAL300025277954 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277954

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277954/0 /scratch/stefan/7808390/working/building/REAL300025277954 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/844
`/scratch/stefan/7808390/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C=CC=CC=C3)C2C1)

`REAL300025277954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277954 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C=CC=CC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 19, 35, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 19, 19, 113, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 222
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: REAL300025277954 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C=CC=CC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 47, 13, 1, 1, 1, 1, 1, 1, 1, 81, 113, 113, 113, 113, 113, 176, 176, 176, 201, 201, 201, 201, 201, 201, 113, 113, 47, 47, 1, 113, 113, 113, 113, 113, 113, 176, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113] 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: 628
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: REAL300025277954 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3C=CC=CC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 11, 25, 57, 98, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 57, 57, 201, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46])
total number of confs: 451
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277954 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277954
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277954/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277954
Building REAL300025277955
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277955'
/scratch/stefan/7808390/working/building/REAL300025277955 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277955

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277955/0 /scratch/stefan/7808390/working/building/REAL300025277955 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/845
`/scratch/stefan/7808390/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277955 none C=C(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 62, 62, 62, 62, 62, 39, 30, 39, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 62, 62, 62, 62, 62, 62, 30, 30, 1, 62, 62, 62] 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])
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: REAL300025277955 none C=C(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 62, 62, 62, 62, 62, 1, 1, 57, 57, 57, 57, 57, 31, 31, 30, 30, 6, 1, 1, 1, 1, 1, 1, 5, 5, 62, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277955 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277955
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277955/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277955
Building REAL300025277956
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277956'
/scratch/stefan/7808390/working/building/REAL300025277956 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277956

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277956/0 /scratch/stefan/7808390/working/building/REAL300025277956 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/846
`/scratch/stefan/7808390/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NS3)C2C1)

`REAL300025277956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277956 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 19, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 1, 1, 10, 10, 86, 1, 1, 1, 1, 1, 1, 6, 18, 18, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
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: REAL300025277956 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 13, 1, 1, 1, 1, 1, 1, 1, 56, 86, 86, 86, 86, 86, 152, 152, 152, 201, 201, 201, 201, 86, 86, 45, 45, 1, 86, 86, 86, 86, 86, 86, 152, 201, 201, 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])
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: REAL300025277956 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NS3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 18, 26, 68, 104, 201, 201, 201, 201, 201, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 18, 18, 68, 68, 201, 18, 18, 18, 18, 18, 18, 6, 1, 1, 18, 18, 18] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277956 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277956
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277956/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277956
Building REAL300025277957
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277957'
/scratch/stefan/7808390/working/building/REAL300025277957 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277957

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277957/0 /scratch/stefan/7808390/working/building/REAL300025277957 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/847
`/scratch/stefan/7808390/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277957 none CCC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [24, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 22, 63, 63, 63, 63, 63, 1, 1, 14, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 14, 14, 63, 1, 1, 1] 131
rigid atoms, others: [43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 50, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 216
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: REAL300025277957 none CCC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 29, 29, 54, 78, 131, 131, 131, 131, 131, 14, 14, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 54, 54, 131, 14, 14, 14] 131
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 36, 26, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 344
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: REAL300025277957 none CCC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 131, 131, 131, 100, 100, 100, 63, 63, 63, 63, 63, 50, 34, 50, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 100, 63, 63, 63, 63, 63, 63, 34, 34, 1, 63, 63, 63] 131
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])
total number of confs: 445
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277957 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277957
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277957/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277957
Building REAL300025277958
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277958'
/scratch/stefan/7808390/working/building/REAL300025277958 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277958

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277958/0 /scratch/stefan/7808390/working/building/REAL300025277958 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/848
`/scratch/stefan/7808390/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025277958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277958 none COCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 19, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 18, 65, 65, 65, 65, 65, 1, 1, 14, 14, 34, 34, 34, 27, 27, 19, 19, 5, 1, 1, 1, 1, 1, 1, 9, 9, 65, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50])
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: REAL300025277958 none COCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 10, 5, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 24, 24, 52, 84, 180, 180, 180, 180, 180, 14, 14, 1, 1, 18, 18, 18, 10, 10, 5, 5, 5, 14, 14, 14, 14, 14, 14, 52, 52, 180, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 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: 481
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277958 none COCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 180, 110, 110, 110, 65, 65, 65, 65, 65, 48, 27, 48, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 180, 180, 201, 201, 201, 201, 201, 188, 188, 110, 65, 65, 65, 65, 65, 65, 27, 27, 1, 65, 65, 65, 180, 180, 180, 180] 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, 50])
total number of confs: 690
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277958 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277958
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277958/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277958
Building REAL300025277959
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277959'
/scratch/stefan/7808390/working/building/REAL300025277959 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277959

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277959/0 /scratch/stefan/7808390/working/building/REAL300025277959 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/849
`/scratch/stefan/7808390/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025277959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277959 none CC(C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 19, 63, 63, 63, 63, 63, 1, 1, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 12, 12, 63, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50, 51, 52])
total number of confs: 172
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277959 none CC(C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 30, 30, 61, 95, 200, 200, 200, 200, 200, 16, 16, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 16, 16, 16, 16, 61, 61, 200, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 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, 47, 48])
total number of confs: 486
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277959 none CC(C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 140, 140, 140, 63, 63, 63, 63, 63, 40, 26, 40, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 63, 63, 63, 63, 63, 63, 26, 26, 1, 63, 63, 63, 200, 200, 200, 200] 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, 52])
total number of confs: 646
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277959 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277959
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277959/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277959
Building REAL300025277960
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277960'
/scratch/stefan/7808390/working/building/REAL300025277960 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277960

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277960/0 /scratch/stefan/7808390/working/building/REAL300025277960 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/850
`/scratch/stefan/7808390/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277960 none COCC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 196, 200, 116, 196, 116, 116, 52, 52, 52, 52, 52, 34, 28, 34, 12, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 200, 200, 200, 200, 196, 196, 196, 196, 116, 52, 52, 52, 52, 52, 52, 28, 28, 1, 52, 52, 52] 201
rigid atoms, others: [49, 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, 50, 51, 52])
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: REAL300025277960 none COCC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 27, 18, 27, 6, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 52, 52, 52, 52, 52, 1, 1, 31, 31, 31, 29, 29, 27, 27, 27, 27, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 6, 6, 52, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277960 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277960
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277960/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277960
Building REAL300025277961
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277961'
/scratch/stefan/7808390/working/building/REAL300025277961 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277961

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277961/0 /scratch/stefan/7808390/working/building/REAL300025277961 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/851
`/scratch/stefan/7808390/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCNC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277961 none O=C(CC1CCNC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 52, 52, 52, 52, 52, 1, 1, 29, 29, 40, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 1, 1, 5, 5, 52, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277961 none O=C(CC1CCNC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40, 40, 40, 52, 52, 73, 116, 201, 201, 201, 201, 201, 40, 40, 6, 6, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 40, 40, 40, 73, 73, 201, 40, 40, 40] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025277961 none O=C(CC1CCNC1=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 8, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 200, 201, 201, 201, 201, 201, 52, 52, 52, 52, 52, 33, 26, 33, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 200, 200, 201, 201, 201, 201, 201, 201, 112, 52, 52, 52, 52, 52, 52, 26, 26, 1, 52, 52, 52] 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])
total number of confs: 736
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277961 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277961
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277961/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277961
Building REAL300025277962
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277962'
/scratch/stefan/7808390/working/building/REAL300025277962 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277962

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277962/0 /scratch/stefan/7808390/working/building/REAL300025277962 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/852
`/scratch/stefan/7808390/working/3D/852' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3COC4)C2C1)

`REAL300025277962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277962 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3COC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 16, 1, 1, 12, 12, 71, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 16, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277962 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3COC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 50, 71, 71, 71, 71, 71, 114, 114, 114, 201, 201, 201, 201, 201, 201, 71, 71, 39, 39, 1, 71, 71, 71, 71, 71, 71, 114, 201, 201, 201, 201, 201, 201, 71, 71, 71] 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: 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: REAL300025277962 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3COC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 30, 65, 105, 201, 201, 201, 201, 201, 16, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 65, 65, 201, 16, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 489
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277962 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277962
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277962/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277962
Building REAL300025277963
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277963'
/scratch/stefan/7808390/working/building/REAL300025277963 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300025277963 as failed and skipping
/scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `/scratch/stefan/7808390/failed'
`/scratch/stefan/7808390/working/building/REAL300025277963' -> `/scratch/stefan/7808390/failed/REAL300025277963'
Building REAL300025277964
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277964'
/scratch/stefan/7808390/working/building/REAL300025277964 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277964

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277964/0 /scratch/stefan/7808390/working/building/REAL300025277964 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/853
`/scratch/stefan/7808390/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025277964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277964 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 17, 75, 75, 75, 75, 75, 1, 1, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 10, 10, 75, 1, 1, 1, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 39, 37, 20, 21, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 164
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277964 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 34, 34, 73, 115, 201, 201, 201, 201, 201, 19, 19, 1, 1, 2, 2, 2, 6, 19, 19, 19, 19, 19, 19, 73, 73, 201, 19, 19, 19, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 22, 23] set([3, 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: 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: REAL300025277964 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 75, 75, 75, 75, 75, 51, 42, 51, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 117, 75, 75, 75, 75, 75, 75, 42, 42, 1, 75, 75, 75, 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])
total number of confs: 700
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277964 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277964
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277964/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277964
Building REAL300025277965
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277965'
/scratch/stefan/7808390/working/building/REAL300025277965 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277965

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277965/0 /scratch/stefan/7808390/working/building/REAL300025277965 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/854
`/scratch/stefan/7808390/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277965 none CC1CCCC1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 48, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 35, 35, 35, 35, 35, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 31, 31, 6, 1, 1, 1, 1, 1, 1, 4, 4, 35, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277965 none CC1CCCC1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 15, 15, 15, 48, 48, 48, 48, 48, 57, 57, 80, 117, 201, 201, 201, 201, 201, 48, 48, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 48, 48, 48, 48, 48, 48, 80, 80, 201, 48, 48, 48] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 37, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025277965 none CC1CCCC1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 83, 83, 83, 35, 35, 35, 35, 35, 25, 22, 25, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 83, 35, 35, 35, 35, 35, 35, 22, 22, 1, 35, 35, 35] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277965 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277965
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277965/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277965
Building REAL300025277966
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277966'
/scratch/stefan/7808390/working/building/REAL300025277966 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277966

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277966/0 /scratch/stefan/7808390/working/building/REAL300025277966 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/855
`/scratch/stefan/7808390/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277966 none CCC(=O)NC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 140, 140, 140, 140, 104, 140, 104, 104, 43, 43, 43, 43, 43, 31, 26, 31, 11, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 104, 43, 43, 43, 43, 43, 43, 26, 26, 1, 43, 43, 43] 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])
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: REAL300025277966 none CCC(=O)NC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 12, 12, 12, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 43, 43, 43, 43, 43, 1, 1, 45, 45, 45, 45, 45, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 5, 5, 43, 1, 1, 1] 201
rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277966 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277966
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277966/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277966
Building REAL300025277967
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277967'
/scratch/stefan/7808390/working/building/REAL300025277967 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277967

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277967/0 /scratch/stefan/7808390/working/building/REAL300025277967 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/856
`/scratch/stefan/7808390/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1=O)

`REAL300025277967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277967 none CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [32, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 21, 65, 65, 65, 65, 65, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 16, 16, 65, 1, 1, 1, 32, 32] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277967 none CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 9, 9, 9, 32, 32, 32, 32, 32, 61, 61, 117, 149, 201, 201, 201, 201, 201, 32, 32, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 117, 117, 201, 32, 32, 32, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 46, 47, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 33, 34, 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: REAL300025277967 none CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 142, 142, 142, 65, 65, 65, 65, 65, 42, 34, 42, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 65, 65, 65, 65, 65, 65, 34, 34, 1, 65, 65, 65, 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])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277967 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277967
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277967/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277967
Building REAL300025277968
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277968'
/scratch/stefan/7808390/working/building/REAL300025277968 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277968

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277968/0 /scratch/stefan/7808390/working/building/REAL300025277968 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/857
`/scratch/stefan/7808390/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277968 none CNC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 113, 113, 113, 49, 49, 49, 49, 49, 32, 28, 32, 12, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 199, 199, 113, 49, 49, 49, 49, 49, 49, 28, 28, 1, 49, 49, 49] 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])
total number of confs: 743
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277968 none CNC(=O)NCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 49, 49, 49, 49, 49, 1, 1, 39, 39, 39, 39, 39, 33, 33, 6, 1, 1, 1, 1, 1, 1, 5, 5, 49, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277968 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277968
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277968/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277968
Building REAL300025277969
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277969'
/scratch/stefan/7808390/working/building/REAL300025277969 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277969

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277969/0 /scratch/stefan/7808390/working/building/REAL300025277969 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/858
`/scratch/stefan/7808390/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCO3)C2C1)

`REAL300025277969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277969 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 16, 32, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 1, 1, 16, 16, 109, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 221
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277969 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 44, 13, 1, 1, 1, 1, 1, 1, 1, 78, 109, 109, 109, 109, 109, 176, 176, 176, 201, 201, 201, 201, 201, 109, 109, 44, 44, 1, 109, 109, 109, 109, 109, 109, 176, 201, 201, 201, 201, 201, 201, 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, 43, 44])
total number of confs: 642
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277969 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 30, 72, 115, 201, 201, 201, 201, 201, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 72, 72, 201, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 35, 42, 43, 44])
total number of confs: 493
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277969 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277969
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277969/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277969
Building REAL300025277970
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277970'
/scratch/stefan/7808390/working/building/REAL300025277970 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277970

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277970/0 /scratch/stefan/7808390/working/building/REAL300025277970 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/859
`/scratch/stefan/7808390/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277970 none CCOCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 167, 149, 138, 87, 87, 87, 47, 47, 47, 47, 47, 33, 29, 33, 11, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 201, 201, 167, 167, 138, 138, 87, 47, 47, 47, 47, 47, 47, 29, 29, 1, 47, 47, 47] 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])
total number of confs: 801
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277970 none CCOCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 22, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 47, 47, 47, 47, 47, 1, 1, 34, 34, 34, 34, 34, 34, 34, 25, 25, 12, 12, 6, 1, 1, 1, 1, 1, 1, 6, 6, 47, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277970 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277970
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277970/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277970
Building REAL300025277971
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277971'
/scratch/stefan/7808390/working/building/REAL300025277971 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277971

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277971/0 /scratch/stefan/7808390/working/building/REAL300025277971 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/860
`/scratch/stefan/7808390/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025277971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277971 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 93, 93, 93, 43, 43, 43, 43, 43, 31, 28, 31, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 201, 201, 191, 191, 93, 43, 43, 43, 43, 43, 43, 28, 28, 1, 43, 43, 43, 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])
total number of confs: 786
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277971 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 43, 43, 43, 43, 43, 1, 1, 44, 44, 44, 44, 44, 44, 44, 31, 31, 6, 1, 1, 1, 1, 1, 1, 5, 5, 43, 1, 1, 1, 44, 44, 44, 44, 44] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 44, 43, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277971 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 5, 15, 15, 15, 44, 44, 44, 44, 44, 53, 53, 77, 106, 201, 201, 201, 201, 201, 44, 44, 1, 1, 1, 3, 3, 3, 3, 5, 5, 15, 44, 44, 44, 44, 44, 44, 77, 77, 201, 44, 44, 44, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 45, 46, 47, 48, 49, 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, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 513
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277971 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277971
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277971/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277971
Building REAL300025277972
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277972'
/scratch/stefan/7808390/working/building/REAL300025277972 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277972

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277972/0 /scratch/stefan/7808390/working/building/REAL300025277972 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/861
`/scratch/stefan/7808390/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025277972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277972 none CC1=NC=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [54, 54, 54, 54, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 53, 53, 53, 53, 53, 1, 1, 54, 54, 54, 54, 54, 21, 21, 4, 1, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277972 none CC1=NC=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 8, 37, 37, 37, 54, 54, 54, 54, 54, 60, 60, 84, 118, 201, 201, 201, 201, 201, 54, 54, 1, 2, 2, 2, 1, 8, 8, 37, 54, 54, 54, 54, 54, 54, 84, 84, 201, 54, 54, 54] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 524
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277972 none CC1=NC=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 177, 90, 90, 90, 53, 53, 53, 53, 53, 45, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 177, 177, 90, 53, 53, 53, 53, 53, 53, 30, 30, 1, 53, 53, 53] 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])
total number of confs: 760
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277972 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277972
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277972/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277972
Building REAL300025277973
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277973'
/scratch/stefan/7808390/working/building/REAL300025277973 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277973

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277973/0 /scratch/stefan/7808390/working/building/REAL300025277973 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/862
`/scratch/stefan/7808390/working/3D/862' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1)

`REAL300025277973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277973 none C[NH+](C)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 4, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 3, 3, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5] 10
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50, 51, 52])
total number of confs: 32
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: REAL300025277973 none C[NH+](C)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 3, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 7, 10, 10, 10, 10, 10, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 5, 5, 5, 5, 5, 5, 6, 6, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1] 10
rigid atoms, others: [1, 4, 5, 47, 48, 49, 50, 51, 52, 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, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 36
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: REAL300025277973 none C[NH+](C)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10] 10
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, 50, 51, 52])
total number of confs: 24
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277973 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277973
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277973/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277973
Building REAL300025277974
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277974'
/scratch/stefan/7808390/working/building/REAL300025277974 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277974

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277974/0 /scratch/stefan/7808390/working/building/REAL300025277974 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/863
`/scratch/stefan/7808390/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277974 none CC(C)(C(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 116, 194, 194, 201, 201, 116, 116, 53, 53, 53, 53, 53, 34, 28, 34, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 194, 194, 194, 194, 194, 194, 201, 201, 116, 53, 53, 53, 53, 53, 53, 28, 28, 1, 53, 53, 53] 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])
total number of confs: 776
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277974 none CC(C)(C(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 21, 21, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 53, 53, 53, 53, 53, 1, 1, 21, 21, 21, 21, 21, 21, 30, 30, 6, 1, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277974 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277974
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277974/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277974
Building REAL300025277975
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277975'
/scratch/stefan/7808390/working/building/REAL300025277975 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277975

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277975/0 /scratch/stefan/7808390/working/building/REAL300025277975 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/864
`/scratch/stefan/7808390/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C)

`REAL300025277975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277975 none CC(C)[C@@H](C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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: [71, 83, 83, 64, 83, 64, 64, 34, 34, 34, 34, 34, 28, 22, 28, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 64, 34, 34, 34, 34, 34, 34, 22, 22, 1, 34, 34, 34, 83, 83, 83, 83, 83, 83] 83
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, 52, 53, 54])
total number of confs: 384
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277975 none CC(C)[C@@H](C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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: [9, 11, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 9, 34, 34, 34, 34, 34, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 7, 7, 34, 1, 1, 1, 11, 11, 11, 11, 11, 11] 83
rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 48, 40, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50, 51, 52, 53, 54])
total number of confs: 110
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277975 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277975
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277975/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277975
Building REAL300025277976
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277976'
/scratch/stefan/7808390/working/building/REAL300025277976 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277976

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277976/0 /scratch/stefan/7808390/working/building/REAL300025277976 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/865
`/scratch/stefan/7808390/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N(C)C=N1)

`REAL300025277976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277976 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 67, 67, 67, 67, 67, 1, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 9, 9, 67, 1, 1, 1, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46])
total number of confs: 136
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277976 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 19, 19, 19, 19, 19, 29, 29, 65, 98, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 65, 65, 201, 19, 19, 19, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 46, 23, 24, 25, 26] set([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, 42, 43, 44, 45])
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: REAL300025277976 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 115, 115, 115, 67, 67, 67, 67, 67, 48, 42, 48, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 115, 67, 67, 67, 67, 67, 67, 42, 42, 1, 67, 67, 67, 201, 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: 505
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277976 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277976
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277976/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277976
Building REAL300025277977
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277977'
/scratch/stefan/7808390/working/building/REAL300025277977 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277977

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277977/0 /scratch/stefan/7808390/working/building/REAL300025277977 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/866
`/scratch/stefan/7808390/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CN=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277977 none O=C(CC1=CN=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 8, 1, 14, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 30, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 63, 63, 63, 63, 63, 1, 1, 30, 30, 45, 45, 5, 1, 1, 1, 1, 1, 1, 9, 9, 63, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 225
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277977 none O=C(CC1=CN=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 8, 1, 14, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [25, 4, 1, 1, 1, 1, 1, 1, 25, 26, 45, 45, 45, 45, 45, 56, 56, 81, 115, 201, 201, 201, 201, 201, 45, 45, 4, 4, 1, 1, 25, 45, 45, 45, 45, 45, 45, 81, 81, 201, 45, 45, 45] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29] set([0, 1, 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: 513
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: REAL300025277977 none O=C(CC1=CN=CS1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 8, 1, 14, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [96, 96, 96, 166, 201, 201, 201, 201, 63, 63, 63, 63, 63, 51, 31, 51, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 166, 166, 201, 201, 96, 63, 63, 63, 63, 63, 63, 31, 31, 1, 63, 63, 63] 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])
total number of confs: 709
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277977 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277977
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277977/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277977
Building REAL300025277978
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277978'
/scratch/stefan/7808390/working/building/REAL300025277978 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277978

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277978/0 /scratch/stefan/7808390/working/building/REAL300025277978 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/867
`/scratch/stefan/7808390/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NN=C3)C2C1)

`REAL300025277978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277978 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 16, 25, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 1, 16, 16, 82, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 163
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: REAL300025277978 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 56, 82, 82, 82, 82, 82, 108, 108, 108, 201, 201, 201, 201, 201, 201, 82, 82, 34, 34, 1, 82, 82, 82, 82, 82, 82, 108, 201, 201, 201, 82, 82, 82] 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: 478
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: REAL300025277978 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC(=O)NN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 14, 29, 68, 102, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 68, 68, 201, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 499
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277978 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277978
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277978/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277978
Building REAL300025277979
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277979'
/scratch/stefan/7808390/working/building/REAL300025277979 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277979

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277979/0 /scratch/stefan/7808390/working/building/REAL300025277979 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/868
`/scratch/stefan/7808390/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC(=O)N1)

`REAL300025277979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277979 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 14, 52, 52, 52, 52, 52, 1, 1, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 9, 9, 52, 1, 1, 1, 27, 27] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277979 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations 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, 27, 27, 27, 27, 27, 38, 38, 74, 109, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 1, 2, 2, 2, 7, 27, 27, 27, 27, 27, 27, 74, 74, 201, 27, 27, 27, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 43, 44, 23, 24, 25, 26] set([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, 42])
total number of confs: 521
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277979 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 106, 106, 106, 52, 52, 52, 52, 52, 37, 31, 37, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 106, 52, 52, 52, 52, 52, 52, 31, 31, 1, 52, 52, 52, 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])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277979 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277979
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277979/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277979
Building REAL300025277980
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277980'
/scratch/stefan/7808390/working/building/REAL300025277980 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277980

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277980/0 /scratch/stefan/7808390/working/building/REAL300025277980 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/869
`/scratch/stefan/7808390/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CC3)C2C1)

`REAL300025277980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025277980 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 36, 36, 14, 14, 1, 1, 6, 6, 48, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36, 36, 14, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300025277980 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 44, 66, 101, 201, 201, 201, 201, 201, 36, 36, 36, 36, 13, 13, 7, 13, 1, 1, 1, 1, 7, 7, 36, 36, 66, 66, 201, 36, 36, 36, 36, 36, 36, 13, 1, 1, 1, 1, 1, 7, 7, 7, 7, 36, 36, 36] 201
rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 479
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277980 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 37, 48, 48, 48, 48, 48, 89, 89, 89, 138, 201, 201, 138, 138, 48, 48, 31, 31, 1, 48, 48, 48, 48, 48, 48, 89, 201, 201, 201, 201, 201, 138, 138, 138, 138, 48, 48, 48] 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: 698
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277980 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 18, 30, 50, 138, 138, 138, 138, 138, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 7, 7, 1, 1, 14, 14, 30, 30, 138, 14, 14, 14, 14, 14, 14, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [41, 42, 43, 44, 16, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 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: 297
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277980 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277980
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277980/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277980
Building REAL300025277981
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277981'
/scratch/stefan/7808390/working/building/REAL300025277981 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277981

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277981/0 /scratch/stefan/7808390/working/building/REAL300025277981 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/870
`/scratch/stefan/7808390/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025277981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277981 none COC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 14, 69, 69, 69, 69, 69, 1, 1, 20, 43, 43, 43, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 8, 8, 69, 1, 1, 1, 20, 20] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47])
total number of confs: 186
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277981 none COC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 11, 20, 20, 20, 20, 20, 31, 31, 63, 104, 201, 201, 201, 201, 201, 20, 20, 1, 6, 6, 6, 1, 1, 1, 1, 11, 20, 20, 20, 20, 20, 20, 63, 63, 201, 20, 20, 20, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 46, 47, 25, 29, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 497
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: REAL300025277981 none COC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 107, 107, 107, 69, 69, 69, 69, 69, 57, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 107, 69, 69, 69, 69, 69, 69, 30, 30, 1, 69, 69, 69, 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])
total number of confs: 681
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277981 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277981
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277981/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277981
Building REAL300025277982
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277982'
/scratch/stefan/7808390/working/building/REAL300025277982 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277982

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277982/0 /scratch/stefan/7808390/working/building/REAL300025277982 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/871
`/scratch/stefan/7808390/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCC(=O)N3)C2C1)

`REAL300025277982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277982 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 15, 28, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 1, 1, 15, 15, 98, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 47, 10, 11, 12, 13, 14, 15, 46, 45, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 209
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: REAL300025277982 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 40, 13, 1, 1, 1, 1, 1, 1, 1, 65, 98, 98, 98, 98, 98, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 98, 98, 40, 40, 1, 98, 98, 98, 98, 98, 98, 156, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98] 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: 636
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: REAL300025277982 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3CCCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 19, 31, 63, 102, 201, 201, 201, 201, 201, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 63, 63, 201, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19] 201
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47])
total number of confs: 488
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277982 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277982
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277982/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277982
Building REAL300025277983
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277983'
/scratch/stefan/7808390/working/building/REAL300025277983 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277983

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277983/0 /scratch/stefan/7808390/working/building/REAL300025277983 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/872
`/scratch/stefan/7808390/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOCC3)C2C1)

`REAL300025277983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277983 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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, 7]
0  hydrogens 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, 10, 20, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 1, 1, 10, 10, 78, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 159
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277983 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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, 7]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 56, 78, 78, 78, 78, 78, 140, 140, 140, 201, 201, 201, 201, 201, 201, 78, 78, 38, 38, 1, 78, 78, 78, 78, 78, 78, 140, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78] 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: 680
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: REAL300025277983 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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, 7]
0  hydrogens 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, 26, 64, 103, 201, 201, 201, 201, 201, 15, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 64, 64, 201, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47])
total number of confs: 512
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277983 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277983
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277983/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277983
Building REAL300025277984
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277984'
/scratch/stefan/7808390/working/building/REAL300025277984 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277984

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277984/0 /scratch/stefan/7808390/working/building/REAL300025277984 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/873
`/scratch/stefan/7808390/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277984 none O=C(CCC1=CNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 19, 19, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 54, 54, 54, 54, 54, 1, 1, 19, 19, 19, 19, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 5, 5, 54, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277984 none O=C(CCC1=CNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 5, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 29, 29, 50, 89, 201, 201, 201, 201, 201, 20, 20, 5, 5, 5, 5, 1, 1, 1, 7, 20, 20, 20, 20, 20, 20, 50, 50, 201, 20, 20, 20] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 481
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277984 none O=C(CCC1=CNC=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [137, 137, 137, 201, 201, 201, 201, 201, 201, 54, 54, 54, 54, 54, 36, 26, 36, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 137, 54, 54, 54, 54, 54, 54, 26, 26, 1, 54, 54, 54] 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])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277984 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277984/1 /scratch/stefan/7808390/working/building/REAL300025277984 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/874
`/scratch/stefan/7808390/working/3D/874' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277984.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277984/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277984 none O=C(CCC1=CN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 24, 31, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 23, 23, 23, 23, 23, 1, 1, 24, 24, 31, 31, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 5, 23, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277984 none O=C(CCC1=CN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 1, 1, 1, 1, 1, 1, 14, 14, 34, 34, 34, 34, 34, 44, 44, 61, 98, 201, 201, 201, 201, 201, 34, 34, 5, 5, 3, 3, 1, 1, 1, 14, 34, 34, 34, 34, 34, 34, 61, 61, 201, 34, 34, 34] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 502
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277984 none O=C(CCC1=CN=CN1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [73, 73, 73, 194, 199, 201, 201, 201, 201, 23, 23, 23, 23, 23, 14, 12, 14, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 194, 194, 199, 199, 201, 201, 201, 73, 23, 23, 23, 23, 23, 23, 12, 12, 1, 23, 23, 23] 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])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277984 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277984
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277984/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277984/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277984
Building REAL300025277985
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277985'
/scratch/stefan/7808390/working/building/REAL300025277985 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025277985

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277985/0 /scratch/stefan/7808390/working/building/REAL300025277985 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/875
`/scratch/stefan/7808390/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1)

`REAL300025277985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277985 none C[N@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 141, 141, 141, 57, 57, 57, 57, 57, 33, 30, 33, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 196, 196, 141, 57, 57, 57, 57, 57, 57, 30, 30, 1, 57, 57, 57, 201, 201, 201, 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, 51, 52])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277985 none C[N@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 57, 57, 57, 57, 57, 1, 1, 30, 34, 34, 34, 30, 30, 30, 23, 23, 6, 1, 1, 1, 1, 1, 1, 7, 7, 57, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277985 none C[N@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 14, 14, 14, 34, 34, 34, 34, 34, 51, 51, 90, 105, 201, 201, 201, 201, 201, 34, 34, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 34, 34, 34, 34, 34, 34, 90, 90, 201, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 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])
total number of confs: 575
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277985 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025277985/1 /scratch/stefan/7808390/working/building/REAL300025277985 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/876
`/scratch/stefan/7808390/working/3D/876' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1)

`REAL300025277985.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025277985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277985/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277985 none C[N@@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 201, 136, 136, 136, 56, 56, 56, 56, 56, 34, 32, 34, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 195, 195, 136, 56, 56, 56, 56, 56, 56, 32, 32, 1, 56, 56, 56, 201, 201, 201, 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, 51, 52])
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: REAL300025277985 none C[N@@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 56, 56, 56, 56, 56, 1, 1, 29, 37, 37, 37, 29, 29, 29, 23, 23, 6, 1, 1, 1, 1, 1, 1, 7, 7, 56, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277985 none C[N@@H+](CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 6, 16, 16, 16, 37, 37, 37, 37, 37, 55, 55, 98, 115, 201, 201, 201, 201, 201, 37, 37, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 37, 37, 37, 37, 37, 37, 98, 98, 201, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 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])
total number of confs: 583
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277985 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277985
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025277985/1.*
0: /scratch/stefan/7808390/working/building/REAL300025277985/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277985
Building REAL300025277986
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277986'
/scratch/stefan/7808390/working/building/REAL300025277986 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277986

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277986/0 /scratch/stefan/7808390/working/building/REAL300025277986 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/877
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1)

`REAL300025277986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277986 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 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, 7, 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: [6, 1, 6, 18, 34, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 1, 1, 18, 18, 125, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
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: REAL300025277986 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 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, 7, 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: [79, 48, 13, 1, 1, 1, 1, 1, 1, 1, 79, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 48, 48, 1, 125, 125, 125, 125, 125, 125, 201, 201, 201, 201, 125, 125, 125] 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: 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: REAL300025277986 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=C(F)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 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, 7, 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: [23, 10, 23, 69, 117, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 69, 201, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277986 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277986
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277986/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277986
Building REAL300025277987
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277987'
/scratch/stefan/7808390/working/building/REAL300025277987 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277987

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277987/0 /scratch/stefan/7808390/working/building/REAL300025277987 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/878
`/scratch/stefan/7808390/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277987 none C=CCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 146, 144, 139, 85, 85, 85, 39, 39, 39, 39, 39, 31, 27, 31, 11, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 146, 146, 139, 139, 85, 39, 39, 39, 39, 39, 39, 27, 27, 1, 39, 39, 39] 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])
total number of confs: 852
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277987 none C=CCCOCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 19, 17, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 39, 39, 39, 39, 39, 1, 1, 33, 33, 33, 29, 29, 19, 19, 11, 11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 39, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277987 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277987
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277987/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277987
Building REAL300025277988
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277988'
/scratch/stefan/7808390/working/building/REAL300025277988 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277988

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277988/0 /scratch/stefan/7808390/working/building/REAL300025277988 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/879
`/scratch/stefan/7808390/working/3D/879' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277988 none C=CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 147, 169, 147, 147, 54, 54, 54, 54, 54, 36, 31, 36, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 169, 169, 169, 169, 147, 54, 54, 54, 54, 54, 54, 31, 31, 1, 54, 54, 54] 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])
total number of confs: 752
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277988 none C=CCOC(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 54, 54, 54, 54, 54, 1, 1, 30, 30, 30, 23, 23, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277988 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277988
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277988/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277988
Building REAL300025277989
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277989'
/scratch/stefan/7808390/working/building/REAL300025277989 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277989

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277989/0 /scratch/stefan/7808390/working/building/REAL300025277989 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/880
`/scratch/stefan/7808390/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277989 none CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [29, 29, 29, 6, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 13, 41, 41, 41, 41, 41, 1, 1, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 8, 8, 41, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277989 none CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 9, 9, 9, 29, 29, 29, 29, 29, 39, 39, 75, 114, 201, 201, 201, 201, 201, 29, 29, 2, 2, 2, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 75, 75, 201, 29, 29, 29] 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: 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: REAL300025277989 none CC1=CN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 130, 201, 201, 98, 98, 98, 41, 41, 41, 41, 41, 28, 25, 28, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 201, 98, 41, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41, 41] 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])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277989 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277989
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277989/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277989
Building REAL300025277990
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277990'
/scratch/stefan/7808390/working/building/REAL300025277990 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277990

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277990/0 /scratch/stefan/7808390/working/building/REAL300025277990 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/881
`/scratch/stefan/7808390/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3(F)F)C2C1)

`REAL300025277990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277990 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 10, 19, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 4, 4, 4, 25, 25, 25, 25, 25, 1, 1, 10, 10, 79, 1, 1, 1, 1, 1, 1, 4, 25, 25, 25, 25, 25, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 41, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277990 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 34, 13, 1, 1, 1, 1, 1, 1, 1, 59, 79, 79, 79, 79, 79, 127, 127, 127, 201, 201, 201, 201, 201, 79, 79, 34, 34, 1, 79, 79, 79, 79, 79, 79, 127, 201, 201, 201, 201, 201, 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, 40, 41, 42, 43])
total number of confs: 677
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277990 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC3(F)F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 25, 34, 66, 104, 201, 201, 201, 201, 201, 25, 25, 25, 25, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 66, 66, 201, 25, 25, 25, 25, 25, 25, 12, 1, 1, 1, 1, 1, 25, 25, 25] 201
rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42, 43])
total number of confs: 498
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277990 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277990
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277990/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277990
Building REAL300025277991
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277991'
/scratch/stefan/7808390/working/building/REAL300025277991 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277991

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277991/0 /scratch/stefan/7808390/working/building/REAL300025277991 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/882
`/scratch/stefan/7808390/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSC=C3)C2C1)

`REAL300025277991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277991 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 39, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 1, 1, 19, 19, 121, 1, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
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: REAL300025277991 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 49, 13, 1, 1, 1, 1, 1, 1, 1, 79, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 121, 121, 49, 49, 1, 121, 121, 121, 121, 121, 121, 201, 201, 201, 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, 39])
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: REAL300025277991 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NSC=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 69, 123, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 69, 69, 201, 10, 10, 10, 10, 10, 10, 4, 1, 1, 10, 10, 10] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 477
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277991 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277991
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277991/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277991
Building REAL300025277992
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277992'
/scratch/stefan/7808390/working/building/REAL300025277992 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277992

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277992/0 /scratch/stefan/7808390/working/building/REAL300025277992 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/883
`/scratch/stefan/7808390/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1)

`REAL300025277992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277992 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 138, 138, 138, 58, 58, 58, 58, 58, 39, 29, 39, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 138, 58, 58, 58, 58, 58, 58, 29, 29, 1, 58, 58, 58, 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])
total number of confs: 777
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277992 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 58, 58, 58, 58, 58, 1, 1, 30, 38, 38, 38, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 6, 6, 58, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277992 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 14, 14, 14, 38, 38, 38, 38, 38, 52, 52, 80, 127, 201, 201, 201, 201, 201, 38, 38, 1, 1, 1, 1, 3, 3, 3, 3, 14, 38, 38, 38, 38, 38, 38, 80, 80, 201, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 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, 42])
total number of confs: 555
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277992 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277992
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277992/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277992
Building REAL300025277993
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277993'
/scratch/stefan/7808390/working/building/REAL300025277993 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277993

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277993/0 /scratch/stefan/7808390/working/building/REAL300025277993 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/884
`/scratch/stefan/7808390/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1C=CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277993 none O=C(CC1C=CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 39, 39, 39, 39, 39, 1, 1, 35, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 1, 1, 1, 1, 1, 1, 4, 4, 39, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277993 none O=C(CC1C=CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 45, 45, 45, 45, 45, 56, 56, 75, 113, 201, 201, 201, 201, 201, 45, 45, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 45, 45, 45, 75, 75, 201, 45, 45, 45] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277993 none O=C(CC1C=CCCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 201, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 28, 24, 28, 11, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 39, 39, 39, 39, 39, 39, 24, 24, 1, 39, 39, 39] 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])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277993 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277993
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277993/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277993
Building REAL300025277994
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277994'
/scratch/stefan/7808390/working/building/REAL300025277994 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277994

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277994/0 /scratch/stefan/7808390/working/building/REAL300025277994 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/885
`/scratch/stefan/7808390/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025277994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277994 none CCOCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 24, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 21, 77, 77, 77, 77, 77, 1, 1, 13, 13, 47, 47, 47, 47, 47, 24, 24, 4, 1, 1, 1, 1, 1, 1, 10, 10, 77, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277994 none CCOCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 8, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 21, 21, 42, 71, 180, 180, 180, 180, 180, 13, 13, 1, 1, 23, 23, 23, 23, 23, 8, 8, 7, 13, 13, 13, 13, 13, 13, 42, 42, 180, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 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: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277994 none CCOCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 112, 112, 112, 77, 77, 77, 77, 77, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 180, 180, 201, 201, 201, 201, 201, 200, 200, 112, 77, 77, 77, 77, 77, 77, 29, 29, 1, 77, 77, 77, 180, 180, 180, 180] 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, 50])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277994 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277994
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277994/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277994
Building REAL300025277995
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277995'
/scratch/stefan/7808390/working/building/REAL300025277995 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277995

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277995/0 /scratch/stefan/7808390/working/building/REAL300025277995 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/886
`/scratch/stefan/7808390/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3O4)C2C1)

`REAL300025277995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277995 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3O4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 14, 28, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1, 14, 14, 101, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 200
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: REAL300025277995 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3O4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 44, 13, 1, 1, 1, 1, 1, 1, 1, 73, 101, 101, 101, 101, 101, 169, 169, 169, 201, 201, 201, 201, 201, 201, 101, 101, 44, 44, 1, 101, 101, 101, 101, 101, 101, 169, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101] 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: 643
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: REAL300025277995 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4C=CC3O4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 14, 27, 60, 104, 201, 201, 201, 201, 201, 14, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 60, 60, 201, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46])
total number of confs: 461
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277995 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277995
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277995/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277995
Building REAL300025277996
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277996'
/scratch/stefan/7808390/working/building/REAL300025277996 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277996

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277996/0 /scratch/stefan/7808390/working/building/REAL300025277996 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/887
`/scratch/stefan/7808390/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(C)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277996 none CCCCC(C)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 132, 172, 172, 132, 132, 45, 45, 45, 45, 45, 31, 25, 31, 11, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 132, 45, 45, 45, 45, 45, 45, 25, 25, 1, 45, 45, 45] 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])
total number of confs: 778
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277996 none CCCCC(C)(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 45, 45, 45, 45, 45, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 45, 1, 1, 1] 201
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 49, 50, 51, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277996 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277996
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277996/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277996
Building REAL300025277997
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277997'
/scratch/stefan/7808390/working/building/REAL300025277997 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277997

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277997/0 /scratch/stefan/7808390/working/building/REAL300025277997 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/888
`/scratch/stefan/7808390/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025277997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277997 none COC1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 18, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 18, 85, 85, 85, 85, 85, 1, 1, 30, 30, 30, 18, 18, 18, 18, 18, 18, 18, 18, 4, 1, 1, 1, 1, 1, 1, 11, 11, 85, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277997 none COC1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 9, 18, 18, 18, 18, 18, 30, 30, 62, 101, 201, 201, 201, 201, 201, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 62, 62, 201, 18, 18, 18] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 37, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025277997 none COC1CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 85, 85, 85, 85, 85, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 85, 85, 85, 85, 85, 85, 30, 30, 1, 85, 85, 85] 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])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277997 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277997
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277997/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277997
Building REAL300025277998
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277998'
/scratch/stefan/7808390/working/building/REAL300025277998 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277998

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277998/0 /scratch/stefan/7808390/working/building/REAL300025277998 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/889
`/scratch/stefan/7808390/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CO1)

`REAL300025277998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277998 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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: [10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 39, 91, 91, 91, 91, 91, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 24, 24, 91, 1, 1, 1, 10, 10] 110
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47])
total number of confs: 210
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277998 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 10, 19, 19, 61, 77, 110, 110, 110, 110, 110, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 61, 61, 110, 10, 10, 10, 1, 1] 110
rigid atoms, others: [0, 1, 2, 3, 4, 32, 46, 47, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 320
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: REAL300025277998 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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, 102, 102, 102, 91, 91, 91, 91, 91, 63, 37, 63, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 110, 110, 110, 110, 110, 110, 110, 110, 110, 102, 91, 91, 91, 91, 91, 91, 37, 37, 1, 91, 91, 91, 110, 110] 110
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])
total number of confs: 338
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277998 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277998
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277998/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277998
Building REAL300025277999
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025277999'
/scratch/stefan/7808390/working/building/REAL300025277999 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025277999

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025277999/0 /scratch/stefan/7808390/working/building/REAL300025277999 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/890
`/scratch/stefan/7808390/working/3D/890' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC4CC43)C2C1)

`REAL300025277999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025277999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025277999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277999 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC4CC43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 13, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 1, 1, 8, 8, 49, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025277999 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC4CC43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 13, 1, 1, 1, 1, 1, 1, 1, 35, 49, 49, 49, 49, 49, 115, 115, 115, 201, 201, 201, 201, 201, 201, 49, 49, 29, 29, 1, 49, 49, 49, 49, 49, 49, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49] 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: 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: REAL300025277999 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC4CC43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 24, 35, 71, 112, 201, 201, 201, 201, 201, 24, 24, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 24, 24, 71, 71, 201, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 516
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025277999 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025277999
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025277999/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025277999
Building REAL300025278000
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278000'
/scratch/stefan/7808390/working/building/REAL300025278000 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278000

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278000/0 /scratch/stefan/7808390/working/building/REAL300025278000 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/891
`/scratch/stefan/7808390/working/3D/891' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC2CC21)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278000 none O=C(CC1CCC2CC21)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 7, 39, 39, 39, 39, 39, 1, 1, 35, 35, 60, 60, 60, 60, 60, 60, 60, 60, 60, 6, 1, 1, 1, 1, 1, 1, 4, 4, 39, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278000 none O=C(CC1CCC2CC21)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 60, 60, 60, 60, 60, 68, 68, 95, 129, 201, 201, 201, 201, 201, 60, 60, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 60, 60, 60, 60, 60, 60, 95, 95, 201, 60, 60, 60] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025278000 none O=C(CC1CCC2CC21)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 194, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 30, 25, 30, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 39, 39, 39, 39, 39, 39, 25, 25, 1, 39, 39, 39] 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])
total number of confs: 778
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278000 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278000
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278000/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278000
Building REAL300025278001
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278001'
/scratch/stefan/7808390/working/building/REAL300025278001 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278001

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278001/0 /scratch/stefan/7808390/working/building/REAL300025278001 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/892
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CCC4CC4C3)C2C1)

`REAL300025278001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278001 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC4CC4C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 14, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 23, 23, 23, 23, 23, 1, 1, 8, 8, 59, 1, 1, 1, 1, 1, 1, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 147
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: REAL300025278001 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC4CC4C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 59, 59, 59, 59, 59, 107, 107, 107, 201, 201, 201, 201, 201, 201, 59, 59, 29, 29, 1, 59, 59, 59, 59, 59, 59, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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, 46, 47, 48, 49, 50])
total number of confs: 666
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: REAL300025278001 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC4CC4C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 65, 101, 201, 201, 201, 201, 201, 23, 23, 23, 23, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 23, 23, 65, 65, 201, 23, 23, 23, 23, 23, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 503
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278001 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278001
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278001/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278001
Building REAL300025278002
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278002'
/scratch/stefan/7808390/working/building/REAL300025278002 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278002

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278002/0 /scratch/stefan/7808390/working/building/REAL300025278002 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/893
`/scratch/stefan/7808390/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278002 none CCC(C)C(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 181, 201, 137, 181, 181, 137, 137, 59, 59, 59, 59, 59, 39, 35, 39, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 137, 59, 59, 59, 59, 59, 59, 35, 35, 1, 59, 59, 59] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 798
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278002 none CCC(C)C(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 59, 59, 59, 59, 59, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 6, 6, 59, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278002 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278002
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278002/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278002
Building REAL300025278003
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278003'
/scratch/stefan/7808390/working/building/REAL300025278003 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278003

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278003/0 /scratch/stefan/7808390/working/building/REAL300025278003 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/894
`/scratch/stefan/7808390/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025278003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278003 none COC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 51, 51, 51, 51, 51, 1, 1, 23, 39, 39, 39, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1, 1, 23, 23] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278003 none COC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 23, 23, 23, 23, 23, 34, 34, 52, 91, 201, 201, 201, 201, 201, 23, 23, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 52, 52, 201, 23, 23, 23, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 49, 50, 35, 26, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 474
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278003 none COC1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 110, 110, 110, 51, 51, 51, 51, 51, 35, 29, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 51, 51, 51, 51, 51, 51, 29, 29, 1, 51, 51, 51, 201, 201] 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])
total number of confs: 632
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278003 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278003
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278003/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278003
Building REAL300025278004
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278004'
/scratch/stefan/7808390/working/building/REAL300025278004 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278004

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278004/0 /scratch/stefan/7808390/working/building/REAL300025278004 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/895
`/scratch/stefan/7808390/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278004 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 18, 43, 43, 43, 43, 43, 1, 1, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 12, 12, 43, 1, 1, 1] 68
rigid atoms, others: [48, 47, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 113
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278004 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 19, 19, 32, 43, 68, 68, 68, 68, 68, 10, 10, 2, 2, 2, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 10, 32, 32, 68, 10, 10, 10] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 32, 33] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 185
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: REAL300025278004 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 66, 68, 66, 66, 43, 43, 43, 43, 43, 35, 29, 35, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 68, 68, 68, 68, 68, 68, 68, 66, 43, 43, 43, 43, 43, 43, 29, 29, 1, 43, 43, 43] 68
rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48])
total number of confs: 223
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278004 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278004
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278004/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278004
Building REAL300025278005
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278005'
/scratch/stefan/7808390/working/building/REAL300025278005 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278005

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278005/0 /scratch/stefan/7808390/working/building/REAL300025278005 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/896
`/scratch/stefan/7808390/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278005 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 8, 8, 8, 6, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 36, 116, 116, 116, 116, 116, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 22, 22, 116, 1, 1, 1] 172
rigid atoms, others: [48, 43, 49, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 50, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 232
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: REAL300025278005 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 24, 24, 68, 101, 172, 172, 172, 172, 172, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 68, 68, 172, 8, 8, 8] 172
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 37] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 440
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: REAL300025278005 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 116, 116, 116, 116, 116, 74, 44, 74, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 116, 116, 116, 116, 116, 116, 44, 44, 1, 116, 116, 116] 172
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50])
total number of confs: 545
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278005 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278005
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278005/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278005
Building REAL300025278006
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278006'
/scratch/stefan/7808390/working/building/REAL300025278006 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278006

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278006/0 /scratch/stefan/7808390/working/building/REAL300025278006 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/897
`/scratch/stefan/7808390/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1C1CC1)

`REAL300025278006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025278006 none CC1C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 36, 126, 126, 126, 126, 126, 1, 1, 11, 11, 15, 15, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 18, 18, 126, 1, 1, 1, 11, 15, 15, 15, 15, 15] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 44, 43, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49, 50])
total number of confs: 245
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.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: REAL300025278006 none CC1C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 15, 15, 15, 15, 15, 29, 29, 55, 97, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 55, 55, 201, 15, 15, 15, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [46, 47, 48, 49, 50, 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, 42, 43, 44, 45])
total number of confs: 452
number of broken/clashed sets: 33
./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278006 none CC1C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 11, 11, 11, 11, 23, 23, 52, 95, 201, 201, 201, 201, 201, 11, 11, 1, 1, 4, 4, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 11, 11, 52, 52, 201, 11, 11, 11, 1, 4, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 45, 23, 24, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50])
total number of confs: 456
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: REAL300025278006 none CC1C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 183, 126, 126, 126, 126, 126, 78, 33, 78, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 126, 126, 126, 126, 126, 126, 33, 33, 1, 126, 126, 126, 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])
total number of confs: 574
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278006 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278006
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278006/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278006
Building REAL300025278007
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278007'
/scratch/stefan/7808390/working/building/REAL300025278007 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278007

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278007/0 /scratch/stefan/7808390/working/building/REAL300025278007 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/898
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CCCC34CC4)C2C1)

`REAL300025278007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278007 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC34CC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 13, 25, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1, 13, 13, 99, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 190
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278007 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC34CC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 66, 99, 99, 99, 99, 99, 166, 166, 166, 201, 201, 201, 201, 201, 201, 99, 99, 43, 43, 1, 99, 99, 99, 99, 99, 99, 166, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 99] 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: 627
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278007 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCCC34CC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 57, 95, 201, 201, 201, 201, 201, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 57, 57, 201, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 463
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278007 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278007
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278007/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278007
Building REAL300025278008
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278008'
/scratch/stefan/7808390/working/building/REAL300025278008 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278008

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278008/0 /scratch/stefan/7808390/working/building/REAL300025278008 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/899
`/scratch/stefan/7808390/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278008 none COCCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 160, 159, 159, 94, 94, 94, 35, 35, 35, 35, 35, 23, 19, 23, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 162, 162, 159, 159, 159, 159, 94, 35, 35, 35, 35, 35, 35, 19, 19, 1, 35, 35, 35] 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])
total number of confs: 898
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278008 none COCCOCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 16, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 35, 35, 35, 35, 35, 1, 1, 23, 23, 23, 23, 23, 18, 18, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 6, 6, 35, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278008 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278008
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278008/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278008
Building REAL300025278009
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278009'
/scratch/stefan/7808390/working/building/REAL300025278009 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278009

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278009/0 /scratch/stefan/7808390/working/building/REAL300025278009 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/900
`/scratch/stefan/7808390/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278009 none CC(C)OCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 201, 101, 101, 101, 37, 37, 37, 37, 37, 25, 22, 25, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 201, 201, 198, 201, 201, 201, 201, 201, 101, 37, 37, 37, 37, 37, 37, 22, 22, 1, 37, 37, 37] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 798
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278009 none CC(C)OCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 17, 16, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 37, 37, 37, 37, 37, 1, 1, 26, 26, 26, 26, 26, 26, 26, 16, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 5, 5, 37, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278009 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278009
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278009/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278009
Building REAL300025278010
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278010'
/scratch/stefan/7808390/working/building/REAL300025278010 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278010

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278010/0 /scratch/stefan/7808390/working/building/REAL300025278010 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/901
`/scratch/stefan/7808390/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278010 none NC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 180, 85, 85, 85, 44, 44, 44, 44, 44, 27, 22, 27, 11, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 187, 193, 193, 193, 180, 180, 85, 44, 44, 44, 44, 44, 44, 22, 22, 1, 44, 44, 44] 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])
total number of confs: 889
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278010 none NC(=O)CCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 33, 37, 21, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 1, 1, 37, 37, 30, 28, 28, 28, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278010 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278010
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278010/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278010
Building REAL300025278011
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278011'
/scratch/stefan/7808390/working/building/REAL300025278011 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278011

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278011/0 /scratch/stefan/7808390/working/building/REAL300025278011 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/902
`/scratch/stefan/7808390/working/3D/902' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+]1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025278011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278011 none C[NH+]1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 21, 63, 63, 63, 63, 63, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 14, 14, 63, 1, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50, 51, 52])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278011 none C[NH+]1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 23, 23, 23, 23, 23, 49, 49, 110, 146, 201, 201, 201, 201, 201, 23, 23, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 110, 110, 201, 23, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 49, 50, 35, 52, 33, 27, 51, 26, 31] set([7, 8, 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, 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: REAL300025278011 none C[NH+]1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 63, 63, 63, 63, 63, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 63, 63, 63, 63, 63, 63, 36, 36, 1, 63, 63, 63, 201, 201, 201, 201] 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, 52])
total number of confs: 644
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278011 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278011
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278011/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278011
Building REAL300025278012
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278012'
/scratch/stefan/7808390/working/building/REAL300025278012 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278012

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278012/0 /scratch/stefan/7808390/working/building/REAL300025278012 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/903
`/scratch/stefan/7808390/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278012 none CCC(CC)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 149, 149, 201, 77, 149, 77, 77, 42, 42, 42, 42, 42, 33, 30, 33, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 201, 201, 149, 201, 201, 201, 201, 201, 149, 149, 149, 149, 77, 42, 42, 42, 42, 42, 42, 30, 30, 1, 42, 42, 42] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 1190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278012 none CCC(CC)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 23, 32, 6, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 42, 42, 42, 42, 42, 1, 1, 32, 32, 32, 32, 31, 23, 32, 32, 32, 32, 32, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 5, 5, 42, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278012 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278012
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278012/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278012
Building REAL300025278013
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278013'
/scratch/stefan/7808390/working/building/REAL300025278013 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278013

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278013/0 /scratch/stefan/7808390/working/building/REAL300025278013 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/904
`/scratch/stefan/7808390/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCCC3)C2C1)

`REAL300025278013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278013 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 11, 24, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 1, 11, 11, 82, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 44, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 180
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: REAL300025278013 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 38, 13, 1, 1, 1, 1, 1, 1, 1, 56, 82, 82, 82, 82, 82, 151, 151, 151, 201, 201, 201, 201, 201, 82, 82, 38, 38, 1, 82, 82, 82, 82, 82, 82, 151, 201, 201, 201, 201, 201, 201, 201, 201, 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, 42, 43, 44, 45, 46])
total number of confs: 650
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: REAL300025278013 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 20, 32, 63, 97, 201, 201, 201, 201, 201, 20, 20, 20, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 63, 63, 201, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [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, 35, 44, 45, 46])
total number of confs: 477
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278013 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278013
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278013/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278013
Building REAL300025278014
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278014'
/scratch/stefan/7808390/working/building/REAL300025278014 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278014

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278014/0 /scratch/stefan/7808390/working/building/REAL300025278014 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/905
`/scratch/stefan/7808390/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278014 none CN1C=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 33, 102, 102, 102, 102, 102, 1, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 18, 18, 102, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 203
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: REAL300025278014 none CN1C=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 15, 15, 15, 15, 15, 28, 28, 64, 99, 201, 201, 201, 201, 201, 15, 15, 2, 2, 2, 1, 1, 7, 15, 15, 15, 15, 15, 15, 64, 64, 201, 15, 15, 15] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 464
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: REAL300025278014 none CN1C=NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 184, 184, 184, 102, 102, 102, 102, 102, 66, 41, 66, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 184, 102, 102, 102, 102, 102, 102, 41, 41, 1, 102, 102, 102] 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])
total number of confs: 588
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278014 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278014
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278014/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278014
Building REAL300025278015
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278015'
/scratch/stefan/7808390/working/building/REAL300025278015 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278015

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278015/0 /scratch/stefan/7808390/working/building/REAL300025278015 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/906
`/scratch/stefan/7808390/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)(C)C)

`REAL300025278015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278015 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 159, 159, 95, 95, 95, 95, 95, 65, 44, 65, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 159, 95, 95, 95, 95, 95, 95, 44, 44, 1, 95, 95, 95, 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])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278015 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 22, 95, 95, 95, 95, 95, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 12, 12, 95, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278015 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278015
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278015/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278015
Building REAL300025278016
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278016'
/scratch/stefan/7808390/working/building/REAL300025278016 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278016

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278016/0 /scratch/stefan/7808390/working/building/REAL300025278016 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/907
`/scratch/stefan/7808390/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C34CCC(CC3)C4)C2C1)

`REAL300025278016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278016 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C34CCC(CC3)C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 18, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 1, 1, 11, 11, 51, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 122
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278016 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C34CCC(CC3)C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 12, 1, 1, 1, 1, 1, 1, 1, 35, 51, 51, 51, 51, 51, 78, 78, 78, 201, 201, 201, 201, 201, 201, 51, 51, 28, 28, 1, 51, 51, 51, 51, 51, 51, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51] 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: 432
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278016 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C34CCC(CC3)C4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 31, 71, 116, 201, 201, 201, 201, 201, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 71, 71, 201, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 515
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278016 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278016
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278016/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278016
Building REAL300025278017
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278017'
/scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025278017

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278017/0 /scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/908
`/scratch/stefan/7808390/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278017 none C[N@@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 5, 5, 6, 1, 1, 1] 7
rigid atoms, others: [45, 43, 15, 41, 10, 11, 12, 13, 14, 44, 16, 50, 51, 52, 46, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 33
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278017 none C[N@@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 6, 6, 7, 5, 5, 5] 7
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])
total number of confs: 27
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: REAL300025278017 none C[N@@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 5, 5, 1, 6, 6, 6] 7
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 12
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278017/1 /scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/909
`/scratch/stefan/7808390/working/3D/909' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278017.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278017/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278017 none C[N@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 20, 46, 46, 46, 46, 46, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 15, 15, 46, 1, 1, 1] 92
rigid atoms, others: [45, 43, 15, 41, 10, 11, 12, 13, 14, 44, 16, 50, 51, 52, 46, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
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: REAL300025278017 none C[N@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 32, 32, 64, 77, 92, 92, 92, 92, 92, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 13, 64, 64, 92, 13, 13, 13] 92
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])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278017 none C[N@H+]1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 92, 92, 92, 92, 91, 91, 91, 46, 46, 46, 46, 46, 35, 29, 35, 12, 1, 1, 1, 1, 1, 1, 1, 46, 46, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 91, 46, 46, 46, 46, 46, 46, 29, 29, 1, 46, 46, 46] 92
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 286
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025278017/2 /scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/910
`/scratch/stefan/7808390/working/3D/910' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278017.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025278017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278017/2/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: REAL300025278017 none CN1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 38, 99, 99, 99, 99, 99, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 23, 23, 99, 1, 1, 1] 151
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 49, 50, 51, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 219
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: REAL300025278017 none CN1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 24, 24, 62, 88, 151, 151, 151, 151, 151, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 62, 62, 151, 9, 9, 9] 151
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 36, 38, 5, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 393
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: REAL300025278017 none CN1CCCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 151, 151, 151, 151, 151, 151, 151, 99, 99, 99, 99, 99, 64, 41, 64, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 99, 99, 99, 99, 99, 99, 41, 41, 1, 99, 99, 99] 151
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])
total number of confs: 481
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278017 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278017
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025278017/2.*
1: /scratch/stefan/7808390/working/building/REAL300025278017/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278017/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278017
Building REAL300025278018
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278018'
/scratch/stefan/7808390/working/building/REAL300025278018 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278018

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278018/0 /scratch/stefan/7808390/working/building/REAL300025278018 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/911
`/scratch/stefan/7808390/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278018 none O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 20, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 34, 34, 34, 34, 34, 1, 1, 20, 20, 47, 47, 47, 47, 6, 1, 1, 1, 1, 1, 1, 8, 8, 34, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278018 none O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 1, 1, 1, 1, 1, 1, 1, 13, 13, 47, 47, 47, 47, 47, 72, 72, 102, 154, 201, 201, 201, 201, 201, 47, 47, 7, 7, 1, 1, 1, 1, 13, 47, 47, 47, 47, 47, 47, 102, 102, 201, 47, 47, 47] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025278018 none O=C(CC1=CC=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [61, 61, 61, 135, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 24, 24, 24, 11, 1, 1, 1, 1, 1, 1, 1, 34, 34, 135, 135, 201, 201, 201, 201, 61, 34, 34, 34, 34, 34, 34, 24, 24, 1, 34, 34, 34] 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])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278018 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278018
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278018/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278018
Building REAL300025278019
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278019'
/scratch/stefan/7808390/working/building/REAL300025278019 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278019

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278019/0 /scratch/stefan/7808390/working/building/REAL300025278019 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/912
`/scratch/stefan/7808390/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)O1)

`REAL300025278019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278019 none CCC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [34, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 84, 84, 84, 84, 84, 1, 1, 12, 34, 34, 34, 34, 34, 13, 13, 6, 1, 1, 1, 1, 1, 1, 7, 7, 84, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025278019 none CCC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 19, 19, 39, 71, 171, 171, 171, 171, 171, 13, 13, 1, 6, 7, 7, 6, 6, 1, 1, 4, 13, 13, 13, 13, 13, 13, 39, 39, 171, 13, 13, 13] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 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: 382
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278019 none CCC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 171, 171, 171, 171, 169, 169, 169, 84, 84, 84, 84, 84, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 171, 201, 201, 201, 201, 201, 171, 171, 169, 84, 84, 84, 84, 84, 84, 31, 31, 1, 84, 84, 84] 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])
total number of confs: 710
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278019 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278019
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278019/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278019
Building REAL300025278020
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278020'
/scratch/stefan/7808390/working/building/REAL300025278020 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278020

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278020/0 /scratch/stefan/7808390/working/building/REAL300025278020 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/913
`/scratch/stefan/7808390/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278020 none CC(F)(F)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 191, 100, 100, 100, 38, 38, 38, 38, 38, 25, 19, 25, 11, 1, 1, 1, 1, 1, 1, 1, 38, 38, 201, 201, 201, 201, 201, 191, 191, 100, 38, 38, 38, 38, 38, 38, 19, 19, 1, 38, 38, 38] 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])
total number of confs: 776
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278020 none CC(F)(F)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [46, 46, 46, 46, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 38, 38, 38, 38, 38, 1, 1, 46, 46, 46, 46, 46, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278020 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278020
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278020/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278020
Building REAL300025278021
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278021'
/scratch/stefan/7808390/working/building/REAL300025278021 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278021

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278021/0 /scratch/stefan/7808390/working/building/REAL300025278021 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/914
`/scratch/stefan/7808390/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(=O)NC3)C2C1)

`REAL300025278021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278021 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(=O)NC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 21, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 23, 23, 23, 23, 23, 1, 1, 11, 11, 82, 1, 1, 1, 1, 1, 1, 4, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 182
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: REAL300025278021 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(=O)NC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 62, 82, 82, 82, 82, 82, 126, 126, 126, 201, 201, 201, 201, 201, 201, 82, 82, 36, 36, 1, 82, 82, 82, 82, 82, 82, 126, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82] 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: 655
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: REAL300025278021 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(=O)NC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 36, 85, 121, 201, 201, 201, 201, 201, 23, 23, 23, 23, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 23, 23, 85, 85, 201, 23, 23, 23, 23, 23, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47])
total number of confs: 535
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278021 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278021
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278021/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278021
Building REAL300025278022
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278022'
/scratch/stefan/7808390/working/building/REAL300025278022 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278022

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278022/0 /scratch/stefan/7808390/working/building/REAL300025278022 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/915
`/scratch/stefan/7808390/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278022 none CCC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 64, 64, 64, 64, 64, 1, 1, 33, 33, 33, 33, 33, 16, 16, 6, 1, 1, 1, 1, 1, 1, 7, 7, 64, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278022 none CCC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 23, 23, 41, 66, 134, 134, 134, 134, 134, 16, 16, 5, 5, 5, 4, 4, 1, 1, 5, 16, 16, 16, 16, 16, 16, 41, 41, 134, 16, 16, 16] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 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: 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: REAL300025278022 none CCC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 134, 134, 134, 134, 134, 120, 120, 120, 64, 64, 64, 64, 64, 41, 30, 41, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 134, 134, 120, 64, 64, 64, 64, 64, 64, 30, 30, 1, 64, 64, 64] 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])
total number of confs: 810
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278022 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278022
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278022/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278022
Building REAL300025278023
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278023'
/scratch/stefan/7808390/working/building/REAL300025278023 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025278023

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278023/0 /scratch/stefan/7808390/working/building/REAL300025278023 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/916
`/scratch/stefan/7808390/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNN=C3)C2C1)

`REAL300025278023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278023 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [5, 1, 5, 23, 44, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 1, 1, 23, 23, 130, 1, 1, 1, 1, 1, 1, 6, 7, 7, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
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: REAL300025278023 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [89, 48, 13, 1, 1, 1, 1, 1, 1, 1, 89, 130, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 130, 130, 48, 48, 1, 130, 130, 130, 130, 130, 130, 201, 201, 201, 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])
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: REAL300025278023 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NNN=C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [19, 7, 19, 70, 114, 201, 201, 201, 201, 201, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 70, 70, 201, 7, 7, 7, 7, 7, 7, 3, 1, 1, 7, 7, 7] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 463
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278023 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278023/1 /scratch/stefan/7808390/working/building/REAL300025278023 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/917
`/scratch/stefan/7808390/working/3D/917' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NN3)C2C1)

`REAL300025278023.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278023/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278023 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 4, 18, 36, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 1, 1, 18, 18, 108, 1, 1, 1, 1, 1, 1, 6, 15, 15, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278023 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [76, 47, 13, 1, 1, 1, 1, 1, 1, 1, 76, 108, 108, 108, 108, 108, 178, 178, 178, 201, 201, 201, 201, 108, 108, 47, 47, 1, 108, 108, 108, 108, 108, 108, 178, 201, 201, 108, 108, 108] 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: 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: REAL300025278023 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=NN3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [27, 15, 27, 67, 112, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 15, 15, 67, 67, 201, 15, 15, 15, 15, 15, 15, 5, 1, 1, 15, 15, 15] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 465
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278023 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278023
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025278023/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278023/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278023
Building REAL300025278024
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278024'
/scratch/stefan/7808390/working/building/REAL300025278024 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278024

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278024/0 /scratch/stefan/7808390/working/building/REAL300025278024 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/918
`/scratch/stefan/7808390/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1)

`REAL300025278024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278024 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 73, 73, 73, 73, 73, 1, 1, 17, 17, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 12, 12, 73, 1, 1, 1, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43])
total number of confs: 146
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278024 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 17, 30, 30, 67, 101, 201, 201, 201, 201, 201, 17, 17, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 67, 67, 201, 17, 17, 17, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 43, 23, 24, 25] set([4, 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])
total number of confs: 515
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: REAL300025278024 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 126, 126, 126, 73, 73, 73, 73, 73, 54, 37, 54, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 201, 126, 73, 73, 73, 73, 73, 73, 37, 37, 1, 73, 73, 73, 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])
total number of confs: 514
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278024 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278024
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278024/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278024
Building REAL300025278025
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278025'
/scratch/stefan/7808390/working/building/REAL300025278025 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278025

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278025/0 /scratch/stefan/7808390/working/building/REAL300025278025 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/919
`/scratch/stefan/7808390/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC(=O)N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278025 none O=C(CC1CCC(=O)N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 62, 62, 62, 62, 62, 1, 1, 33, 33, 47, 47, 47, 47, 47, 47, 6, 1, 1, 1, 1, 1, 1, 5, 5, 62, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
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: REAL300025278025 none O=C(CC1CCC(=O)N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 18, 18, 47, 47, 47, 47, 47, 56, 56, 78, 118, 201, 201, 201, 201, 201, 47, 47, 5, 5, 1, 1, 1, 1, 1, 1, 18, 47, 47, 47, 47, 47, 47, 78, 78, 201, 47, 47, 47] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: REAL300025278025 none O=C(CC1CCC(=O)N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 199, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 38, 29, 38, 12, 1, 1, 1, 1, 1, 1, 1, 62, 62, 199, 199, 201, 201, 201, 201, 201, 201, 125, 62, 62, 62, 62, 62, 62, 29, 29, 1, 62, 62, 62] 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])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278025 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278025
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278025/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278025
Building REAL300025278026
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278026'
/scratch/stefan/7808390/working/building/REAL300025278026 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278026

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278026/0 /scratch/stefan/7808390/working/building/REAL300025278026 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/920
`/scratch/stefan/7808390/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025278026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278026 none CNC(=O)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 18, 59, 59, 59, 59, 59, 1, 1, 23, 23, 31, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 14, 14, 59, 1, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46, 47])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278026 none CNC(=O)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 5, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 42, 42, 99, 136, 199, 199, 199, 199, 199, 23, 23, 1, 1, 5, 5, 5, 5, 6, 23, 23, 23, 23, 23, 23, 99, 99, 199, 23, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [2, 4, 5, 44, 45, 46, 47, 25, 26] set([0, 1, 3, 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])
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: REAL300025278026 none CNC(=O)C1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 201, 119, 119, 119, 59, 59, 59, 59, 59, 39, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 199, 199, 201, 201, 201, 201, 119, 59, 59, 59, 59, 59, 59, 33, 33, 1, 59, 59, 59, 199, 199, 199, 199] 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: 617
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278026 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278026
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278026/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278026
Building REAL300025278027
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278027'
/scratch/stefan/7808390/working/building/REAL300025278027 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278027

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278027/0 /scratch/stefan/7808390/working/building/REAL300025278027 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/921
`/scratch/stefan/7808390/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025278027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278027 none COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 24, 104, 104, 104, 104, 104, 1, 1, 13, 13, 43, 43, 43, 25, 25, 4, 1, 1, 1, 1, 1, 1, 13, 13, 104, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46, 47])
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: REAL300025278027 none COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 21, 21, 47, 79, 186, 186, 186, 186, 186, 13, 13, 1, 1, 18, 18, 18, 7, 7, 7, 13, 13, 13, 13, 13, 13, 47, 47, 186, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 44, 45, 46, 47, 24, 25] set([0, 1, 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, 43])
total number of confs: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278027 none COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 138, 138, 138, 104, 104, 104, 104, 104, 76, 32, 76, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 186, 186, 201, 201, 201, 201, 201, 138, 104, 104, 104, 104, 104, 104, 32, 32, 1, 104, 104, 104, 186, 186, 186, 186] 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: 648
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278027 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278027
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278027/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278027
Building REAL300025278028
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278028'
/scratch/stefan/7808390/working/building/REAL300025278028 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278028

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278028/0 /scratch/stefan/7808390/working/building/REAL300025278028 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/922
`/scratch/stefan/7808390/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278028 none COCC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 118, 200, 200, 118, 118, 56, 56, 56, 56, 56, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 200, 118, 56, 56, 56, 56, 56, 56, 29, 29, 1, 56, 56, 56] 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])
total number of confs: 774
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278028 none COCC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 23, 16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 56, 56, 56, 56, 56, 1, 1, 32, 32, 32, 23, 23, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 5, 5, 56, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278028 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278028
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278028/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278028
Building REAL300025278029
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278029'
/scratch/stefan/7808390/working/building/REAL300025278029 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278029

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278029/0 /scratch/stefan/7808390/working/building/REAL300025278029 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/923
`/scratch/stefan/7808390/working/3D/923' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278029 none O=C(CCC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 25, 30, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 29, 29, 29, 29, 29, 1, 1, 25, 25, 30, 30, 35, 35, 6, 1, 1, 1, 1, 1, 1, 5, 5, 29, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 180
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278029 none O=C(CCC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 5, 3, 1, 1, 1, 1, 1, 1, 14, 14, 35, 35, 35, 35, 35, 45, 45, 65, 101, 201, 201, 201, 201, 201, 35, 35, 5, 5, 3, 3, 1, 1, 14, 35, 35, 35, 35, 35, 35, 65, 65, 201, 35, 35, 35] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278029 none O=C(CCC1=NOC=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 8, 12, 1, 1, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [97, 97, 97, 193, 199, 201, 201, 201, 201, 29, 29, 29, 29, 29, 19, 17, 19, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29, 193, 193, 199, 199, 201, 201, 97, 29, 29, 29, 29, 29, 29, 17, 17, 1, 29, 29, 29] 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])
total number of confs: 793
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278029 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278029
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278029/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278029
Building REAL300025278030
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278030'
/scratch/stefan/7808390/working/building/REAL300025278030 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278030

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278030/0 /scratch/stefan/7808390/working/building/REAL300025278030 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/924
`/scratch/stefan/7808390/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025278030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278030 none CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 47, 123, 123, 123, 123, 123, 1, 1, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 27, 27, 123, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 260
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278030 none CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 4, 13, 13, 13, 13, 13, 34, 34, 100, 142, 201, 201, 201, 201, 201, 13, 13, 1, 2, 2, 2, 1, 4, 13, 13, 13, 13, 13, 13, 100, 100, 201, 13, 13, 13] 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])
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: REAL300025278030 none CN1N=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1 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', 'C.3', 'C.3', 'N.am', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 123, 123, 123, 123, 123, 77, 42, 77, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 123, 42, 42, 1, 123, 123, 123] 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])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278030 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278030
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278030/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278030
Building REAL300025278031
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278031'
/scratch/stefan/7808390/working/building/REAL300025278031 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278031

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278031/0 /scratch/stefan/7808390/working/building/REAL300025278031 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/925
`/scratch/stefan/7808390/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CS1)

`REAL300025278031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278031 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 21, 94, 94, 94, 94, 94, 1, 1, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 11, 11, 94, 1, 1, 1, 12] 153
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278031 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
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, 5, 5, 5, 12, 12, 12, 12, 12, 21, 21, 50, 79, 153, 153, 153, 153, 153, 12, 12, 1, 1, 2, 2, 2, 1, 5, 12, 12, 12, 12, 12, 12, 50, 50, 153, 12, 12, 12, 1] 153
rigid atoms, others: [0, 1, 2, 3, 4, 43, 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: 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: REAL300025278031 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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
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, 113, 113, 113, 94, 94, 94, 94, 94, 78, 55, 78, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 153, 153, 153, 153, 153, 153, 113, 94, 94, 94, 94, 94, 94, 55, 55, 1, 94, 94, 94, 153] 153
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: 446
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278031 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278031
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278031/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278031
Building REAL300025278032
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278032'
/scratch/stefan/7808390/working/building/REAL300025278032 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278032

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278032/0 /scratch/stefan/7808390/working/building/REAL300025278032 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/926
`/scratch/stefan/7808390/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOCC1)

`REAL300025278032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278032 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 74, 74, 74, 74, 74, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 11, 11, 74, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278032 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 2, 2, 2, 11, 11, 11, 11, 11, 23, 23, 56, 91, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 56, 56, 201, 11, 11, 11, 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: 464
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278032 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 118, 118, 118, 74, 74, 74, 74, 74, 46, 42, 46, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 118, 74, 74, 74, 74, 74, 74, 42, 42, 1, 74, 74, 74, 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])
total number of confs: 686
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278032 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278032
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278032/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278032
Building REAL300025278033
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278033'
/scratch/stefan/7808390/working/building/REAL300025278033 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278033

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278033/0 /scratch/stefan/7808390/working/building/REAL300025278033 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/927
`/scratch/stefan/7808390/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278033 none CC(C)CC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 201, 69, 69, 69, 33, 33, 33, 33, 33, 25, 24, 25, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 69, 33, 33, 33, 33, 33, 33, 24, 24, 1, 33, 33, 33] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
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: REAL300025278033 none CC(C)CC(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 41, 32, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 33, 33, 33, 33, 33, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 32, 6, 1, 1, 1, 1, 1, 1, 5, 5, 33, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278033 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278033
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278033/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278033
Building REAL300025278034
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278034'
/scratch/stefan/7808390/working/building/REAL300025278034 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025278034

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278034/0 /scratch/stefan/7808390/working/building/REAL300025278034 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/928
`/scratch/stefan/7808390/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278034 none CC1=CN=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 37, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 58, 58, 58, 58, 58, 1, 1, 37, 37, 37, 37, 37, 18, 18, 4, 1, 1, 1, 1, 1, 1, 6, 6, 58, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
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: REAL300025278034 none CC1=CN=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 28, 28, 28, 37, 37, 37, 37, 37, 45, 45, 83, 124, 201, 201, 201, 201, 201, 37, 37, 2, 2, 2, 1, 1, 7, 7, 28, 37, 37, 37, 37, 37, 37, 83, 83, 201, 37, 37, 37] 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: 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: REAL300025278034 none CC1=CN=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 172, 93, 93, 93, 58, 58, 58, 58, 58, 51, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 172, 172, 93, 58, 58, 58, 58, 58, 58, 30, 30, 1, 58, 58, 58] 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])
total number of confs: 743
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278034 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278034/1 /scratch/stefan/7808390/working/building/REAL300025278034 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/929
`/scratch/stefan/7808390/working/3D/929' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C[NH+]=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278034.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278034/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278034 none CC1=C[NH+]=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [57, 57, 57, 57, 57, 57, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 41, 41, 41, 41, 41, 1, 1, 57, 57, 57, 57, 57, 26, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 41, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 47, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
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: REAL300025278034 none CC1=C[NH+]=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 22, 22, 22, 57, 57, 57, 57, 57, 79, 79, 119, 132, 201, 201, 201, 201, 201, 57, 57, 2, 2, 2, 1, 1, 6, 6, 22, 57, 57, 57, 57, 57, 57, 119, 119, 201, 57, 57, 57] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025278034 none CC1=C[NH+]=CN1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 189, 110, 110, 110, 41, 41, 41, 41, 41, 28, 26, 28, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 189, 189, 110, 41, 41, 41, 41, 41, 41, 26, 26, 1, 41, 41, 41] 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])
total number of confs: 719
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278034 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278034
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025278034/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278034/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278034
Building REAL300025278035
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278035'
/scratch/stefan/7808390/working/building/REAL300025278035 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278035

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278035/0 /scratch/stefan/7808390/working/building/REAL300025278035 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/930
`/scratch/stefan/7808390/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278035 none O=C(CCC(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 15, 15, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [119, 119, 119, 198, 201, 201, 201, 50, 50, 50, 50, 50, 33, 31, 33, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 198, 198, 201, 201, 201, 119, 50, 50, 50, 50, 50, 50, 31, 31, 1, 50, 50, 50] 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])
total number of confs: 779
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278035 none O=C(CCC(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 15, 15, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 27, 28, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 50, 50, 50, 50, 50, 1, 1, 27, 27, 33, 33, 34, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278035 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278035
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278035/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278035
Building REAL300025278036
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278036'
/scratch/stefan/7808390/working/building/REAL300025278036 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278036

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278036/0 /scratch/stefan/7808390/working/building/REAL300025278036 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/931
`/scratch/stefan/7808390/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1)

`REAL300025278036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278036 none COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 34, 108, 108, 108, 108, 108, 1, 1, 11, 11, 11, 32, 32, 32, 17, 17, 5, 1, 1, 1, 1, 1, 1, 18, 18, 108, 1, 1, 1, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49, 50])
total number of confs: 268
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: REAL300025278036 none COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 19, 19, 49, 86, 188, 188, 188, 188, 188, 11, 11, 1, 1, 1, 13, 13, 13, 6, 6, 5, 11, 11, 11, 11, 11, 11, 49, 49, 188, 11, 11, 11, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 24, 25, 26] set([0, 1, 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])
total number of confs: 449
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: REAL300025278036 none COCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 160, 160, 160, 108, 108, 108, 108, 108, 73, 31, 73, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 188, 188, 188, 201, 201, 201, 201, 201, 160, 108, 108, 108, 108, 108, 108, 31, 31, 1, 108, 108, 108, 188, 188, 188, 188, 188, 188] 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, 50])
total number of confs: 650
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278036 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278036
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278036/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278036
Building REAL300025278037
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278037'
/scratch/stefan/7808390/working/building/REAL300025278037 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278037

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278037/0 /scratch/stefan/7808390/working/building/REAL300025278037 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/932
`/scratch/stefan/7808390/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(F)F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278037 none CC(CC(F)F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 156, 201, 201, 201, 201, 156, 156, 65, 65, 65, 65, 65, 41, 33, 41, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 156, 65, 65, 65, 65, 65, 65, 33, 33, 1, 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])
total number of confs: 671
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278037 none CC(CC(F)F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 23, 27, 33, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 65, 65, 65, 65, 65, 1, 1, 23, 23, 23, 23, 27, 27, 33, 6, 1, 1, 1, 1, 1, 1, 6, 6, 65, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278037 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278037
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278037/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278037
Building REAL300025278038
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278038'
/scratch/stefan/7808390/working/building/REAL300025278038 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278038

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278038/0 /scratch/stefan/7808390/working/building/REAL300025278038 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/933
`/scratch/stefan/7808390/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025278038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278038 none CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 49, 49, 49, 49, 49, 1, 1, 38, 38, 38, 38, 38, 24, 24, 4, 1, 1, 1, 1, 1, 1, 5, 5, 49, 1, 1, 1, 38, 38, 38, 38] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46])
total number of confs: 201
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278038 none CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 6, 19, 19, 19, 38, 38, 38, 38, 38, 57, 57, 81, 113, 201, 201, 201, 201, 201, 38, 38, 1, 1, 2, 2, 2, 6, 6, 19, 38, 38, 38, 38, 38, 38, 81, 81, 201, 38, 38, 38, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 23, 24] set([3, 4, 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: 554
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: REAL300025278038 none CC1(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 172, 87, 87, 87, 49, 49, 49, 49, 49, 35, 29, 35, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 172, 172, 87, 49, 49, 49, 49, 49, 49, 29, 29, 1, 49, 49, 49, 201, 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: 785
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278038 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278038
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278038/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278038
Building REAL300025278039
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278039'
/scratch/stefan/7808390/working/building/REAL300025278039 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278039

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278039/0 /scratch/stefan/7808390/working/building/REAL300025278039 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/934
`/scratch/stefan/7808390/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CNC(=O)C1)

`REAL300025278039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278039 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 24, 93, 93, 93, 93, 93, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 11, 11, 93, 1, 1, 1, 15, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47])
total number of confs: 178
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: REAL300025278039 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 27, 27, 58, 100, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 5, 15, 15, 15, 15, 15, 15, 58, 58, 201, 15, 15, 15, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 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: 470
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278039 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need 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, 93, 93, 93, 93, 93, 65, 43, 65, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 137, 93, 93, 93, 93, 93, 93, 43, 43, 1, 93, 93, 93, 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])
total number of confs: 649
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278039 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278039
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278039/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278039
Building REAL300025278040
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278040'
/scratch/stefan/7808390/working/building/REAL300025278040 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278040

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278040/0 /scratch/stefan/7808390/working/building/REAL300025278040 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/935
`/scratch/stefan/7808390/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC2CC2C1)

`REAL300025278040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278040 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 60, 60, 60, 60, 60, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 9, 9, 60, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278040 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 4, 16, 16, 16, 16, 16, 27, 27, 66, 107, 201, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 1, 2, 2, 2, 4, 16, 16, 16, 16, 16, 16, 66, 66, 201, 16, 16, 16, 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: 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: REAL300025278040 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 92, 92, 92, 60, 60, 60, 60, 60, 42, 36, 42, 12, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 92, 60, 60, 60, 60, 60, 60, 36, 36, 1, 60, 60, 60, 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])
total number of confs: 648
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278040 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278040
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278040/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278040
Building REAL300025278041
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278041'
/scratch/stefan/7808390/working/building/REAL300025278041 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278041

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278041/0 /scratch/stefan/7808390/working/building/REAL300025278041 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/936
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3(CCF)CC3)C2C1)

`REAL300025278041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278041 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(CCF)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 5, 8, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 26, 31, 9, 9, 1, 1, 5, 5, 46, 1, 1, 1, 1, 1, 1, 5, 26, 26, 31, 31, 9, 9, 9, 9, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 44, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 191
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: REAL300025278041 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(CCF)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 25, 12, 1, 1, 1, 1, 1, 1, 1, 31, 46, 46, 46, 46, 46, 90, 90, 90, 143, 201, 201, 143, 143, 46, 46, 25, 25, 1, 46, 46, 46, 46, 46, 46, 90, 201, 201, 201, 201, 143, 143, 143, 143, 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, 44, 45, 46])
total number of confs: 826
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: REAL300025278041 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(CCF)CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 16, 28, 46, 143, 143, 143, 143, 143, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 6, 11, 1, 1, 9, 9, 28, 28, 143, 9, 9, 9, 9, 9, 9, 4, 6, 6, 11, 11, 1, 1, 1, 1, 9, 9, 9] 201
rigid atoms, others: [40, 41, 42, 43, 16, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 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: 344
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278041 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278041
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278041/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278041
Building REAL300025278042
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278042'
/scratch/stefan/7808390/working/building/REAL300025278042 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278042

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278042/0 /scratch/stefan/7808390/working/building/REAL300025278042 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/937
`/scratch/stefan/7808390/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278042 none COCC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 177, 201, 201, 123, 123, 123, 61, 61, 61, 61, 61, 41, 33, 41, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 123, 61, 61, 61, 61, 61, 61, 33, 33, 1, 61, 61, 61] 201
rigid atoms, others: [49, 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, 50, 51, 52])
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: REAL300025278042 none COCC(C)(C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 23, 14, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 61, 61, 61, 61, 61, 1, 1, 33, 33, 33, 30, 30, 23, 23, 23, 23, 23, 23, 14, 14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 61, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 240
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278042 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278042
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278042/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278042
Building REAL300025278043
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278043'
/scratch/stefan/7808390/working/building/REAL300025278043 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278043

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278043/0 /scratch/stefan/7808390/working/building/REAL300025278043 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/938
`/scratch/stefan/7808390/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278043 none O=C(COCC(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 15, 15, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [83, 83, 83, 158, 176, 201, 201, 201, 36, 36, 36, 36, 36, 28, 26, 28, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 158, 158, 201, 201, 201, 83, 36, 36, 36, 36, 36, 36, 26, 26, 1, 36, 36, 36] 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])
total number of confs: 758
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278043 none O=C(COCC(F)F)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 15, 15, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 14, 22, 28, 34, 34, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 36, 36, 36, 36, 36, 1, 1, 14, 14, 28, 28, 34, 5, 1, 1, 1, 1, 1, 1, 6, 6, 36, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278043 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278043
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278043/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278043
Building REAL300025278044
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278044'
/scratch/stefan/7808390/working/building/REAL300025278044 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025278044

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278044/0 /scratch/stefan/7808390/working/building/REAL300025278044 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/939
`/scratch/stefan/7808390/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025278044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278044 none C[N@@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 35, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 18, 69, 69, 69, 69, 69, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 6, 1, 1, 1, 1, 1, 1, 13, 13, 69, 1, 1, 1, 35, 35] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 52])
total number of confs: 238
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278044 none C[N@@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 13, 13, 13, 35, 35, 35, 35, 35, 52, 52, 94, 125, 201, 201, 201, 201, 201, 35, 35, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 13, 35, 35, 35, 35, 35, 35, 94, 94, 201, 35, 35, 35, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 52, 33, 27, 51, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025278044 none C[N@@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 69, 69, 69, 69, 69, 41, 30, 41, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 69, 69, 69, 69, 69, 69, 30, 30, 1, 69, 69, 69, 201, 201] 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, 52])
total number of confs: 696
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278044 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278044/1 /scratch/stefan/7808390/working/building/REAL300025278044 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/940
`/scratch/stefan/7808390/working/3D/940' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025278044.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278044/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278044 none C[N@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 7, 7, 7, 7, 7, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 4, 4, 7, 1, 1, 1, 3, 3] 7
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 52])
total number of confs: 30
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278044 none C[N@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 7, 7, 7, 7, 7, 3, 3, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 7, 3, 3, 3, 1, 1] 7
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 52, 33, 27, 51, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 29
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278044 none C[N@H+]1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7] 7
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])
total number of confs: 18
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278044 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278044
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025278044/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278044/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278044
Building REAL300025278045
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278045'
/scratch/stefan/7808390/working/building/REAL300025278045 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278045

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278045/0 /scratch/stefan/7808390/working/building/REAL300025278045 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/941
`/scratch/stefan/7808390/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278045 none CN1C=NC=C1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [34, 34, 34, 34, 34, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 42, 42, 42, 42, 42, 1, 1, 34, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 5, 42, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 180
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278045 none CN1C=NC=C1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 11, 11, 11, 34, 34, 34, 34, 34, 48, 48, 72, 116, 201, 201, 201, 201, 201, 34, 34, 2, 2, 2, 1, 1, 3, 3, 11, 34, 34, 34, 34, 34, 34, 72, 72, 201, 34, 34, 34] 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: 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: REAL300025278045 none CN1C=NC=C1CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 121, 121, 121, 42, 42, 42, 42, 42, 26, 22, 26, 10, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 121, 42, 42, 42, 42, 42, 42, 22, 22, 1, 42, 42, 42] 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])
total number of confs: 753
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278045 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278045
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278045/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278045
Building REAL300025278046
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278046'
/scratch/stefan/7808390/working/building/REAL300025278046 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278046

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278046/0 /scratch/stefan/7808390/working/building/REAL300025278046 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/942
`/scratch/stefan/7808390/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025278046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278046 none CCN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 24, 87, 87, 87, 87, 87, 1, 1, 8, 15, 15, 15, 15, 15, 8, 5, 1, 1, 1, 1, 1, 1, 14, 14, 87, 1, 1, 1, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 198
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: REAL300025278046 none CCN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 8, 8, 8, 16, 16, 33, 53, 130, 130, 130, 130, 130, 8, 8, 1, 5, 5, 5, 5, 5, 1, 3, 8, 8, 8, 8, 8, 8, 33, 33, 130, 8, 8, 8, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 46, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 293
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: REAL300025278046 none CCN1C=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 8, 1, 8, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 130, 130, 130, 130, 87, 87, 87, 87, 87, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 130, 201, 201, 201, 201, 201, 130, 130, 87, 87, 87, 87, 87, 87, 29, 29, 1, 87, 87, 87, 130] 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: 829
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278046 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278046
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278046/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278046
Building REAL300025278047
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278047'
/scratch/stefan/7808390/working/building/REAL300025278047 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278047

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278047/0 /scratch/stefan/7808390/working/building/REAL300025278047 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/943
`/scratch/stefan/7808390/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C)

`REAL300025278047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278047 none CCC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 201, 167, 167, 167, 74, 74, 74, 74, 74, 45, 35, 45, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 74, 74, 74, 74, 74, 74, 35, 35, 1, 74, 74, 74, 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])
total number of confs: 706
number of broken/clashed sets: 169
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278047 none CCC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 74, 74, 74, 74, 74, 1, 1, 22, 24, 24, 24, 30, 30, 30, 30, 30, 22, 6, 1, 1, 1, 1, 1, 1, 8, 8, 74, 1, 1, 1, 24, 24, 24, 24, 24, 24] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 45, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51])
total number of confs: 277
number of broken/clashed sets: 169
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278047 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278047
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278047/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278047
Building REAL300025278048
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278048'
/scratch/stefan/7808390/working/building/REAL300025278048 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278048

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278048/0 /scratch/stefan/7808390/working/building/REAL300025278048 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/944
`/scratch/stefan/7808390/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CCC3)C2C1)

`REAL300025278048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025278048 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 10, 17, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 24, 24, 14, 14, 14, 1, 1, 10, 10, 75, 1, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 181
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.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: REAL300025278048 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 69, 107, 201, 201, 201, 201, 201, 25, 25, 25, 25, 13, 13, 7, 13, 1, 1, 1, 1, 7, 7, 7, 25, 25, 69, 69, 201, 25, 25, 25, 25, 25, 25, 13, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 25, 25, 25] 201
rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 518
number of broken/clashed sets: 25
./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278048 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 53, 75, 75, 75, 75, 75, 130, 130, 130, 194, 201, 201, 194, 194, 194, 75, 75, 37, 37, 1, 75, 75, 75, 75, 75, 75, 130, 201, 201, 201, 201, 201, 194, 194, 194, 194, 194, 194, 75, 75, 75] 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: 662
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: REAL300025278048 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(C4CC4)CCC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 45, 72, 194, 194, 194, 194, 194, 14, 14, 14, 14, 6, 6, 1, 6, 1, 1, 7, 7, 1, 1, 1, 14, 14, 45, 45, 194, 14, 14, 14, 14, 14, 14, 6, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [42, 43, 44, 45, 46, 47, 16, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50])
total number of confs: 410
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278048 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278048
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278048/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278048
Building REAL300025278049
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278049'
/scratch/stefan/7808390/working/building/REAL300025278049 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278049

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278049/0 /scratch/stefan/7808390/working/building/REAL300025278049 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/945
`/scratch/stefan/7808390/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1)

`REAL300025278049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278049 none CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [182, 70, 182, 70, 70, 34, 34, 34, 34, 34, 27, 23, 27, 11, 1, 1, 1, 1, 1, 1, 1, 34, 34, 182, 201, 201, 201, 182, 182, 182, 182, 182, 182, 70, 34, 34, 34, 34, 34, 34, 23, 23, 1, 34, 34, 34, 201, 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: 776
number of broken/clashed sets: 144
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278049 none CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 34, 34, 34, 34, 34, 1, 1, 26, 37, 37, 37, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 4, 4, 34, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 45, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 182
number of broken/clashed sets: 144
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278049 none CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 10, 10, 10, 37, 37, 37, 37, 37, 47, 47, 68, 107, 201, 201, 201, 201, 201, 37, 37, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 10, 37, 37, 37, 37, 37, 37, 68, 68, 201, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 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, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 519
number of broken/clashed sets: 144
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278049 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278049
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278049/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278049
Building REAL300025278050
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278050'
/scratch/stefan/7808390/working/building/REAL300025278050 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278050

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278050/0 /scratch/stefan/7808390/working/building/REAL300025278050 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/946
`/scratch/stefan/7808390/working/3D/946' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1)

`REAL300025278050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278050 none COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 170, 170, 170, 83, 83, 83, 83, 83, 52, 38, 52, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 171, 201, 201, 201, 171, 171, 171, 171, 170, 83, 83, 83, 83, 83, 83, 38, 38, 1, 83, 83, 83, 201, 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: 651
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278050 none COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 83, 83, 83, 83, 83, 1, 1, 13, 23, 23, 23, 14, 14, 14, 13, 6, 1, 1, 1, 1, 1, 1, 7, 7, 83, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 21, 22, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278050 none COC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 7, 7, 7, 23, 23, 23, 23, 23, 32, 32, 58, 90, 201, 201, 201, 201, 201, 23, 23, 1, 1, 1, 1, 6, 6, 6, 5, 7, 23, 23, 23, 23, 23, 23, 58, 58, 201, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 44, 45, 46, 47, 48, 49, 50, 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, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278050 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278050
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278050/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278050
Building REAL300025278051
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278051'
/scratch/stefan/7808390/working/building/REAL300025278051 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278051

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278051/0 /scratch/stefan/7808390/working/building/REAL300025278051 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/947
`/scratch/stefan/7808390/working/3D/947' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSN=N3)C2C1)

`REAL300025278051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278051 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSN=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 19, 41, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 1, 1, 19, 19, 125, 1, 1, 1, 1, 1, 1, 6, 9, 1, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31] set([0, 35, 2, 3, 4, 5, 6, 7, 8, 9, 34, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27])
total number of confs: 227
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278051 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSN=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 51, 13, 1, 1, 1, 1, 1, 1, 1, 85, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 125, 125, 51, 51, 1, 125, 125, 125, 125, 125, 125, 201, 201, 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])
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: REAL300025278051 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSN=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 9, 20, 69, 123, 201, 201, 201, 201, 201, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 69, 69, 201, 9, 9, 9, 9, 9, 9, 4, 1, 9, 9, 9] 201
rigid atoms, others: [35, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278051 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278051
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278051/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278051
Building REAL300025278052
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278052'
/scratch/stefan/7808390/working/building/REAL300025278052 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278052

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278052/0 /scratch/stefan/7808390/working/building/REAL300025278052 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/948
`/scratch/stefan/7808390/working/3D/948' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1)

`REAL300025278052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278052 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 80, 80, 80, 80, 80, 1, 1, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 12, 12, 80, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21, 41, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 159
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278052 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 4, 11, 11, 11, 11, 11, 23, 23, 59, 93, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 11, 59, 59, 201, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25] set([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: 488
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278052 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 80, 80, 80, 80, 80, 55, 38, 55, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 114, 80, 80, 80, 80, 80, 80, 38, 38, 1, 80, 80, 80, 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])
total number of confs: 633
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278052 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278052
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278052/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278052
Building REAL300025278053
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278053'
/scratch/stefan/7808390/working/building/REAL300025278053 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278053

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278053/0 /scratch/stefan/7808390/working/building/REAL300025278053 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/949
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3=CN=CO3)C2C1)

`REAL300025278053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278053 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [6, 1, 6, 21, 43, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 1, 1, 21, 21, 126, 1, 1, 1, 1, 1, 1, 6, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 33, 10, 11, 12, 13, 14, 15, 23, 24, 39, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36])
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: REAL300025278053 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [85, 47, 13, 1, 1, 1, 1, 1, 1, 1, 85, 126, 126, 126, 126, 126, 194, 194, 194, 201, 201, 201, 201, 126, 126, 47, 47, 1, 126, 126, 126, 126, 126, 126, 194, 201, 201, 126, 126, 126] 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: 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: REAL300025278053 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CN=CO3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 14, 26, 73, 123, 201, 201, 201, 201, 201, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 14, 14, 73, 73, 201, 14, 14, 14, 14, 14, 14, 4, 1, 1, 14, 14, 14] 201
rigid atoms, others: [35, 36, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 470
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278053 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278053
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278053/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278053
Building REAL300025278054
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278054'
/scratch/stefan/7808390/working/building/REAL300025278054 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278054

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278054/0 /scratch/stefan/7808390/working/building/REAL300025278054 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/950
`/scratch/stefan/7808390/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278054 none O=C(CCN1C=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 22, 24, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 36, 36, 36, 36, 36, 1, 1, 22, 22, 24, 24, 44, 44, 44, 6, 1, 1, 1, 1, 1, 1, 5, 5, 36, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278054 none O=C(CCN1C=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 2, 1, 1, 1, 1, 1, 1, 16, 15, 44, 44, 44, 44, 44, 58, 58, 83, 123, 201, 201, 201, 201, 201, 44, 44, 6, 6, 2, 2, 1, 1, 1, 16, 44, 44, 44, 44, 44, 44, 83, 83, 201, 44, 44, 44] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025278054 none O=C(CCN1C=CN=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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: [83, 83, 83, 113, 115, 201, 201, 201, 201, 36, 36, 36, 36, 36, 24, 20, 24, 11, 1, 1, 1, 1, 1, 1, 1, 36, 36, 113, 113, 115, 115, 201, 201, 201, 83, 36, 36, 36, 36, 36, 36, 20, 20, 1, 36, 36, 36] 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])
total number of confs: 585
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278054 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278054
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278054/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278054
Building REAL300025278055
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278055'
/scratch/stefan/7808390/working/building/REAL300025278055 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278055

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278055/0 /scratch/stefan/7808390/working/building/REAL300025278055 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/951
`/scratch/stefan/7808390/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278055 none CC1=NN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 19, 73, 73, 73, 73, 73, 1, 1, 17, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 12, 12, 73, 1, 1, 1] 164
rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 44, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278055 none CC1=NN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 17, 28, 28, 63, 89, 164, 164, 164, 164, 164, 17, 17, 2, 2, 2, 1, 1, 8, 17, 17, 17, 17, 17, 17, 63, 63, 164, 17, 17, 17] 164
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])
total number of confs: 440
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: REAL300025278055 none CC1=NN=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 164, 164, 164, 164, 119, 119, 119, 73, 73, 73, 73, 73, 53, 38, 53, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 164, 164, 164, 164, 164, 119, 73, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 73] 164
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])
total number of confs: 461
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278055 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278055
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278055/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278055
Building REAL300025278056
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278056'
/scratch/stefan/7808390/working/building/REAL300025278056 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278056

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278056/0 /scratch/stefan/7808390/working/building/REAL300025278056 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/952
`/scratch/stefan/7808390/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C(C)O1)

`REAL300025278056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278056 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C(C)O1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 6, 6, 6, 6, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 2, 2, 6, 1, 1, 1, 7, 7, 7, 7] 9
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 46, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50])
total number of confs: 30
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278056 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C(C)O1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 7, 7, 7, 1, 2, 2, 2] 9
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 24, 25, 26, 30, 31] set([5, 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, 48, 49, 50])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278056 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C(C)O1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 9, 9, 9, 9] 9
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])
total number of confs: 17
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278056 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278056
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278056/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278056
Building REAL300025278057
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278057'
/scratch/stefan/7808390/working/building/REAL300025278057 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278057

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278057/0 /scratch/stefan/7808390/working/building/REAL300025278057 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/953
`/scratch/stefan/7808390/working/3D/953' -> `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)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278057 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 16, 18, 18, 16, 16, 16, 3, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 13, 13, 13, 13, 13, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 3, 1, 1, 1, 1, 1, 1, 4, 4, 13, 1, 1, 1] 40
rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 50, 51, 52, 46, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278057 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 16, 16, 16, 22, 22, 27, 35, 40, 40, 40, 40, 40, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 11, 16, 16, 16, 16, 16, 16, 27, 27, 40, 16, 16, 16] 40
rigid atoms, others: [1, 4, 5, 38, 7, 8, 9, 39, 6] 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, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
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: REAL300025278057 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 15, 40, 15, 15, 13, 13, 13, 13, 13, 13, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15, 13, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13, 13] 40
rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52])
total number of confs: 105
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278057 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278057
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278057/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278057
Building REAL300025278058
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278058'
/scratch/stefan/7808390/working/building/REAL300025278058 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278058

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278058/0 /scratch/stefan/7808390/working/building/REAL300025278058 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/954
`/scratch/stefan/7808390/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025278058 none CC1CC1C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 21, 21, 21, 21, 21, 32, 32, 52, 94, 201, 201, 201, 201, 201, 21, 21, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 21, 21, 21, 21, 21, 21, 52, 52, 201, 21, 21, 21] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 3, 36, 37] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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.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: REAL300025278058 none CC1CC1C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 112, 112, 112, 51, 51, 51, 51, 51, 36, 28, 36, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 51, 51, 51, 51, 51, 51, 28, 28, 1, 51, 51, 51] 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])
total number of confs: 606
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278058 none CC1CC1C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 10, 10, 10, 30, 30, 30, 30, 30, 41, 41, 61, 102, 201, 201, 201, 201, 201, 30, 30, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 61, 61, 201, 30, 30, 30] 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, 47, 48, 49, 50])
total number of confs: 504
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: REAL300025278058 none CC1CC1C1CC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 51, 51, 51, 51, 51, 1, 1, 30, 30, 30, 30, 30, 30, 30, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 162
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278058 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278058
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278058/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278058
Building REAL300025278059
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278059'
/scratch/stefan/7808390/working/building/REAL300025278059 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278059

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278059/0 /scratch/stefan/7808390/working/building/REAL300025278059 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/955
`/scratch/stefan/7808390/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1)

`REAL300025278059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278059 none CCC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [25, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 78, 78, 78, 78, 78, 1, 1, 8, 8, 25, 25, 25, 25, 25, 8, 6, 1, 1, 1, 1, 1, 1, 8, 8, 78, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278059 none CCC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [6, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 13, 13, 28, 54, 134, 134, 134, 134, 134, 8, 8, 1, 1, 7, 7, 7, 6, 6, 1, 4, 8, 8, 8, 8, 8, 8, 28, 28, 134, 8, 8, 8] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 25, 26] set([0, 6, 7, 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, 44, 45])
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: REAL300025278059 none CCC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=NO1 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', 'C.3', 'C.3', 'N.am', '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, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 134, 134, 134, 134, 134, 134, 78, 78, 78, 78, 78, 46, 29, 46, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 134, 134, 201, 201, 201, 201, 201, 134, 134, 78, 78, 78, 78, 78, 78, 29, 29, 1, 78, 78, 78] 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])
total number of confs: 833
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278059 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278059
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278059/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278059
Building REAL300025278060
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278060'
/scratch/stefan/7808390/working/building/REAL300025278060 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278060

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278060/0 /scratch/stefan/7808390/working/building/REAL300025278060 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/956
`/scratch/stefan/7808390/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)C)

`REAL300025278060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278060 none CCC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)C 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 180, 84, 84, 84, 44, 44, 44, 44, 44, 32, 30, 32, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 191, 201, 201, 201, 201, 201, 201, 201, 191, 180, 180, 84, 44, 44, 44, 44, 44, 44, 30, 30, 1, 44, 44, 44, 201, 201, 201, 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, 53, 54])
total number of confs: 835
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: REAL300025278060 none CCC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)C 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 44, 44, 44, 44, 44, 1, 1, 41, 46, 46, 46, 46, 46, 46, 46, 42, 30, 30, 6, 1, 1, 1, 1, 1, 1, 6, 6, 44, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 201
rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 46, 47, 40, 41, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 295
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278060 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278060
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278060/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278060
Building REAL300025278061
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278061'
/scratch/stefan/7808390/working/building/REAL300025278061 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278061

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278061/0 /scratch/stefan/7808390/working/building/REAL300025278061 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/957
`/scratch/stefan/7808390/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278061 none C[NH+](C)CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 197, 197, 166, 136, 162, 117, 117, 117, 59, 59, 59, 59, 59, 47, 31, 47, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 197, 197, 197, 197, 197, 197, 197, 197, 164, 158, 162, 162, 162, 162, 117, 59, 59, 59, 59, 59, 59, 31, 31, 1, 59, 59, 59] 197
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 985
number of broken/clashed sets: 196
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278061 none C[NH+](C)CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [34, 30, 34, 34, 22, 11, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 59, 59, 59, 59, 59, 1, 1, 34, 34, 34, 34, 34, 34, 30, 30, 18, 18, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 9, 9, 59, 1, 1, 1] 197
rigid atoms, others: [16, 11, 47, 15, 44, 10, 43, 12, 13, 14, 45, 48, 52, 46, 54, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 286
number of broken/clashed sets: 196
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278061 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278061
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278061/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278061
Building REAL300025278062
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278062'
/scratch/stefan/7808390/working/building/REAL300025278062 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278062

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278062/0 /scratch/stefan/7808390/working/building/REAL300025278062 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/958
`/scratch/stefan/7808390/working/3D/958' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=C1)

`REAL300025278062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278062 none C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=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', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 128, 128, 128, 128, 128, 1, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 27, 27, 128, 1, 1, 1, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278062 none C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=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', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 1, 4, 4, 4, 11, 11, 11, 11, 11, 32, 32, 102, 145, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 11, 102, 102, 201, 11, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 26, 27, 28, 29, 30] set([7, 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: 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: REAL300025278062 none C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N=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', 'C.3', 'C.3', 'N.am', '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']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 128, 128, 128, 128, 128, 82, 42, 82, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 128, 42, 42, 1, 128, 128, 128, 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])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278062 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278062
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278062/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278062
Building REAL300025278063
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278063'
/scratch/stefan/7808390/working/building/REAL300025278063 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278063

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278063/0 /scratch/stefan/7808390/working/building/REAL300025278063 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/959
`/scratch/stefan/7808390/working/3D/959' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCC(=O)N3)C2C1)

`REAL300025278063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278063 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 9, 16, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 28, 1, 1, 9, 9, 75, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278063 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 51, 75, 75, 75, 75, 75, 156, 156, 156, 201, 201, 201, 201, 201, 201, 75, 75, 43, 43, 1, 75, 75, 75, 75, 75, 75, 156, 201, 201, 201, 201, 201, 75, 75, 75] 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: 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: REAL300025278063 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@@H]3CCC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 28, 38, 75, 111, 201, 201, 201, 201, 201, 28, 28, 28, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 28, 28, 75, 75, 201, 28, 28, 28, 28, 28, 28, 10, 1, 1, 1, 1, 1, 28, 28, 28] 201
rigid atoms, others: [37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 504
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278063 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278063
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278063/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278063
Building REAL300025278064
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278064'
/scratch/stefan/7808390/working/building/REAL300025278064 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278064

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278064/0 /scratch/stefan/7808390/working/building/REAL300025278064 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/960
`/scratch/stefan/7808390/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1CC[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025278064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278064 none C[C@H]1CC[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 17, 52, 52, 52, 52, 52, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 13, 13, 52, 1, 1, 1, 32, 32, 32, 32] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50, 51, 52])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278064 none C[C@H]1CC[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 32, 32, 32, 32, 32, 49, 49, 112, 143, 201, 201, 201, 201, 201, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 32, 32, 112, 112, 201, 32, 32, 32, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 5, 34, 49, 50, 35, 52, 51, 27, 28, 29, 30, 31] set([8, 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, 47, 48])
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: REAL300025278064 none C[C@H]1CC[C@H](C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 108, 201, 108, 108, 52, 52, 52, 52, 52, 32, 32, 32, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 52, 52, 52, 52, 52, 52, 32, 32, 1, 52, 52, 52, 201, 201, 201, 201] 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, 50, 51, 52])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278064 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278064
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278064/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278064
Building REAL300025278065
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278065'
/scratch/stefan/7808390/working/building/REAL300025278065 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278065

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278065/0 /scratch/stefan/7808390/working/building/REAL300025278065 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/961
`/scratch/stefan/7808390/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C)

`REAL300025278065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278065 none CC(C)C(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C 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.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [162, 201, 201, 160, 160, 160, 80, 80, 80, 80, 80, 48, 37, 48, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 80, 80, 80, 80, 80, 80, 37, 37, 1, 80, 80, 80, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [45, 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, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 1017
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: REAL300025278065 none CC(C)C(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)[NH+](C)C 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.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 13, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 80, 80, 80, 80, 80, 1, 1, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 13, 6, 1, 1, 1, 1, 1, 1, 7, 7, 80, 1, 1, 1, 13, 13, 13, 13, 13, 13] 201
rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 12, 46, 47, 48, 40, 41, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50, 51, 52, 53, 54])
total number of confs: 200
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278065 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278065
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278065/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278065
Building REAL300025278066
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278066'
/scratch/stefan/7808390/working/building/REAL300025278066 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025278066

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278066/0 /scratch/stefan/7808390/working/building/REAL300025278066 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/962
`/scratch/stefan/7808390/working/3D/962' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@H+](C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278066 none CCC[N@H+](C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 103, 103, 103, 44, 44, 44, 44, 44, 33, 28, 33, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 44, 44, 44, 44, 44, 44, 28, 28, 1, 44, 44, 44] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 778
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: REAL300025278066 none CCC[N@H+](C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 21, 21, 21, 21, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 44, 44, 44, 44, 44, 1, 1, 31, 31, 31, 31, 31, 29, 29, 21, 21, 21, 21, 21, 20, 20, 6, 1, 1, 1, 1, 1, 1, 7, 7, 44, 1, 1, 1] 201
rigid atoms, others: [16, 11, 47, 15, 44, 10, 43, 12, 13, 14, 45, 48, 52, 46, 54, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 210
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278066 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278066/1 /scratch/stefan/7808390/working/building/REAL300025278066 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/963
`/scratch/stefan/7808390/working/3D/963' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@@H+](C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278066.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278066/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278066 none CCC[N@@H+](C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 109, 109, 109, 47, 47, 47, 47, 47, 34, 30, 34, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 47, 47, 47, 47, 47, 47, 30, 30, 1, 47, 47, 47] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 778
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: REAL300025278066 none CCC[N@@H+](C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 26, 19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 47, 47, 47, 47, 47, 1, 1, 27, 27, 27, 27, 27, 26, 26, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 7, 7, 47, 1, 1, 1] 201
rigid atoms, others: [16, 11, 47, 15, 44, 10, 43, 12, 13, 14, 45, 48, 52, 46, 54, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51])
total number of confs: 192
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278066 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278066
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025278066/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278066/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278066
Building REAL300025278067
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278067'
/scratch/stefan/7808390/working/building/REAL300025278067 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025278067

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278067/0 /scratch/stefan/7808390/working/building/REAL300025278067 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/964
`/scratch/stefan/7808390/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@H+](C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278067 none CCC[N@H+](C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 45, 34, 45, 45, 19, 19, 19, 14, 14, 14, 14, 14, 14, 14, 14, 12, 1, 1, 1, 1, 1, 1, 1, 14, 14, 46, 46, 46, 46, 46, 46, 46, 45, 45, 45, 34, 34, 19, 14, 14, 14, 14, 14, 14, 14, 14, 1, 14, 14, 14] 46
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])
total number of confs: 190
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278067 none CCC[N@H+](C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [22, 18, 15, 10, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 4, 14, 14, 14, 14, 14, 1, 1, 22, 22, 22, 22, 22, 18, 18, 15, 15, 15, 10, 10, 4, 1, 1, 1, 1, 1, 1, 3, 3, 14, 1, 1, 1] 46
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 49, 50, 51, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 127
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278067 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278067/1 /scratch/stefan/7808390/working/building/REAL300025278067 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/965
`/scratch/stefan/7808390/working/3D/965' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@@H+](C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278067.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278067/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278067 none CCC[N@@H+](C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 183, 195, 195, 114, 114, 114, 42, 42, 42, 42, 42, 27, 27, 27, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 183, 183, 114, 42, 42, 42, 42, 42, 42, 27, 27, 1, 42, 42, 42] 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])
total number of confs: 786
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: REAL300025278067 none CCC[N@@H+](C)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 38, 25, 38, 38, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 8, 42, 42, 42, 42, 42, 1, 1, 54, 54, 54, 54, 54, 44, 44, 38, 38, 38, 25, 25, 6, 1, 1, 1, 1, 1, 1, 6, 6, 42, 1, 1, 1] 201
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 49, 50, 51, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 318
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278067 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278067
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025278067/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278067/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278067
Building REAL300025278068
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278068'
/scratch/stefan/7808390/working/building/REAL300025278068 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278068

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278068/0 /scratch/stefan/7808390/working/building/REAL300025278068 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/966
`/scratch/stefan/7808390/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(C)(C)C)

`REAL300025278068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278068 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 60, 60, 60, 60, 60, 39, 30, 39, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 60, 60, 60, 60, 60, 60, 30, 30, 1, 60, 60, 60, 201, 201, 201, 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, 53, 54])
total number of confs: 791
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: REAL300025278068 none CC(CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 60, 60, 60, 60, 60, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 29, 29, 6, 1, 1, 1, 1, 1, 1, 6, 6, 60, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 45, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 245
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278068 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278068
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278068/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278068
Building REAL300025278069
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278069'
/scratch/stefan/7808390/working/building/REAL300025278069 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278069

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278069/0 /scratch/stefan/7808390/working/building/REAL300025278069 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/967
`/scratch/stefan/7808390/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1)

`REAL300025278069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278069 none CC1=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 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: [22, 22, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 24, 24, 24, 24, 24, 1, 1, 22, 22, 22, 22, 22, 22, 17, 17, 4, 1, 1, 1, 1, 1, 1, 5, 5, 24, 1, 1, 1, 22, 22] 55
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278069 none CC1=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 18, 18, 18, 22, 22, 22, 22, 22, 22, 22, 25, 30, 55, 55, 55, 55, 55, 22, 22, 1, 1, 1, 2, 2, 2, 6, 6, 18, 22, 22, 22, 22, 22, 22, 25, 25, 55, 22, 22, 22, 1, 1] 55
rigid atoms, others: [0, 1, 2, 3, 45, 46, 24, 25, 26] set([4, 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])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278069 none CC1=C(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 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, 53, 30, 30, 30, 24, 24, 24, 24, 24, 24, 21, 24, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 55, 55, 55, 55, 55, 55, 53, 53, 30, 24, 24, 24, 24, 24, 24, 21, 21, 1, 24, 24, 24, 55, 55] 55
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])
total number of confs: 219
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278069 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278069
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278069/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278069
Building REAL300025278070
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278070'
/scratch/stefan/7808390/working/building/REAL300025278070 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278070

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278070/0 /scratch/stefan/7808390/working/building/REAL300025278070 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/968
`/scratch/stefan/7808390/working/3D/968' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278070 none CC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 31, 109, 109, 109, 109, 109, 1, 1, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 17, 17, 109, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 209
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: REAL300025278070 none CC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 8, 8, 8, 17, 17, 17, 17, 17, 33, 33, 70, 112, 201, 201, 201, 201, 201, 17, 17, 2, 2, 2, 1, 1, 8, 17, 17, 17, 17, 17, 17, 70, 70, 201, 17, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 487
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: REAL300025278070 none CC1=NNC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 181, 181, 181, 109, 109, 109, 109, 109, 75, 43, 75, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 181, 109, 109, 109, 109, 109, 109, 43, 43, 1, 109, 109, 109] 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])
total number of confs: 581
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278070 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278070
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278070/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278070
Building REAL300025278071
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278071'
/scratch/stefan/7808390/working/building/REAL300025278071 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278071

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278071/0 /scratch/stefan/7808390/working/building/REAL300025278071 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/969
`/scratch/stefan/7808390/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=C1)

`REAL300025278071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278071 none C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 11, 6, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 30, 106, 106, 106, 106, 106, 1, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 15, 15, 106, 1, 1, 1, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278071 none C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 3, 3, 3, 11, 11, 11, 11, 11, 22, 22, 61, 122, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 11, 11, 61, 61, 201, 11, 11, 11, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 26, 27, 28, 29, 30] set([7, 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: 481
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278071 none C#CC1=CC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 106, 106, 106, 106, 106, 71, 47, 71, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 106, 47, 47, 1, 106, 106, 106, 201, 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: 620
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278071 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278071
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278071/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278071
Building REAL300025278072
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278072'
/scratch/stefan/7808390/working/building/REAL300025278072 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025278072

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278072/0 /scratch/stefan/7808390/working/building/REAL300025278072 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/970
`/scratch/stefan/7808390/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NN=N1)

`REAL300025278072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278072 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 49, 49, 49, 49, 49, 1, 1, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 9, 9, 49, 1, 1, 1, 22] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 39, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42])
total number of confs: 120
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278072 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 22, 22, 22, 22, 22, 35, 35, 74, 111, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 74, 74, 201, 22, 22, 22, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 23, 24, 25] set([4, 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])
total number of confs: 524
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: REAL300025278072 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 80, 80, 80, 49, 49, 49, 49, 49, 33, 30, 33, 12, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 80, 49, 49, 49, 49, 49, 49, 30, 30, 1, 49, 49, 49, 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])
total number of confs: 432
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278072 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278072/1 /scratch/stefan/7808390/working/building/REAL300025278072 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/971
`/scratch/stefan/7808390/working/3D/971' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278072.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278072/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278072 none CC1=NNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 27, 91, 91, 91, 91, 91, 1, 1, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 14, 14, 91, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 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: REAL300025278072 none CC1=NNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 13, 13, 13, 13, 13, 23, 23, 64, 112, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 4, 13, 13, 13, 13, 13, 13, 64, 64, 201, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 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: 474
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278072 none CC1=NNN=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 91, 91, 91, 91, 91, 57, 40, 57, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 40, 40, 1, 91, 91, 91] 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])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278072 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278072
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
1: /scratch/stefan/7808390/working/building/REAL300025278072/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278072/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278072
Building REAL300025278073
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278073'
/scratch/stefan/7808390/working/building/REAL300025278073 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278073

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278073/0 /scratch/stefan/7808390/working/building/REAL300025278073 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/972
`/scratch/stefan/7808390/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278073 none CCCC(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 165, 137, 165, 165, 137, 137, 62, 62, 62, 62, 62, 40, 33, 40, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 165, 137, 62, 62, 62, 62, 62, 62, 33, 33, 1, 62, 62, 62] 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])
total number of confs: 780
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278073 none CCCC(OC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 62, 62, 62, 62, 62, 1, 1, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 62, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278073 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278073
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278073/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278073
Building REAL300025278074
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278074'
/scratch/stefan/7808390/working/building/REAL300025278074 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278074

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278074/0 /scratch/stefan/7808390/working/building/REAL300025278074 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/973
`/scratch/stefan/7808390/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278074 none C=C(C)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 123, 201, 201, 123, 123, 70, 70, 70, 70, 70, 48, 35, 48, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 70, 70, 70, 70, 70, 70, 35, 35, 1, 70, 70, 70] 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])
total number of confs: 826
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: REAL300025278074 none C=C(C)C(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 21, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 70, 70, 70, 70, 70, 1, 1, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 7, 7, 70, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 182
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278074 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278074
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278074/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278074
Building REAL300025278075
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278075'
/scratch/stefan/7808390/working/building/REAL300025278075 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278075

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278075/0 /scratch/stefan/7808390/working/building/REAL300025278075 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/974
`/scratch/stefan/7808390/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278075 none CC(CC(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 144, 201, 201, 201, 201, 144, 144, 63, 63, 63, 63, 63, 38, 33, 38, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 201, 201, 144, 63, 63, 63, 63, 63, 63, 33, 33, 1, 63, 63, 63] 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])
total number of confs: 733
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278075 none CC(CC(N)=O)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 21, 27, 33, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 63, 63, 63, 63, 63, 1, 1, 21, 21, 21, 21, 27, 27, 33, 33, 6, 1, 1, 1, 1, 1, 1, 6, 6, 63, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278075 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278075
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278075/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278075
Building REAL300025278076
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278076'
/scratch/stefan/7808390/working/building/REAL300025278076 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278076

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278076/0 /scratch/stefan/7808390/working/building/REAL300025278076 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/975
`/scratch/stefan/7808390/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278076 none NC(=O)C1CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 34, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 62, 62, 62, 62, 62, 1, 1, 34, 34, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 6, 6, 62, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278076 none NC(=O)C1CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 22, 22, 22, 22, 22, 38, 38, 65, 108, 201, 201, 201, 201, 201, 22, 22, 8, 8, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 22, 22, 65, 65, 201, 22, 22, 22] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278076 none NC(=O)C1CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.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: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 133, 133, 133, 62, 62, 62, 62, 62, 38, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 133, 62, 62, 62, 62, 62, 62, 29, 29, 1, 62, 62, 62] 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])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278076 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278076
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278076/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278076
Building REAL300025278077
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278077'
/scratch/stefan/7808390/working/building/REAL300025278077 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278077

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278077/0 /scratch/stefan/7808390/working/building/REAL300025278077 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/976
`/scratch/stefan/7808390/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC3=O)C2C1)

`REAL300025278077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278077 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC3=O)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 9, 16, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 1, 9, 9, 76, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 25, 25, 25, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278077 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC3=O)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 45, 13, 1, 1, 1, 1, 1, 1, 1, 53, 76, 76, 76, 76, 76, 166, 166, 166, 201, 201, 201, 201, 201, 76, 76, 45, 45, 1, 76, 76, 76, 76, 76, 76, 166, 201, 201, 201, 201, 201, 201, 76, 76, 76] 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])
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: REAL300025278077 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCNC3=O)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 25, 36, 68, 106, 201, 201, 201, 201, 201, 25, 25, 25, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 68, 68, 201, 25, 25, 25, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 35, 42, 43, 44])
total number of confs: 511
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278077 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278077
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278077/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278077
Building REAL300025278078
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278078'
/scratch/stefan/7808390/working/building/REAL300025278078 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278078

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278078/0 /scratch/stefan/7808390/working/building/REAL300025278078 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/977
`/scratch/stefan/7808390/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278078 none CN1C(=O)NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 28, 28, 28, 28, 28, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 59, 59, 59, 59, 59, 1, 1, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 9, 9, 59, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 44, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 137
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: REAL300025278078 none CN1C(=O)NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 9, 9, 9, 28, 28, 28, 28, 28, 38, 38, 72, 106, 201, 201, 201, 201, 201, 28, 28, 2, 2, 2, 1, 1, 9, 28, 28, 28, 28, 28, 28, 72, 72, 201, 28, 28, 28] 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])
total number of confs: 515
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: REAL300025278078 none CN1C(=O)NC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 132, 132, 132, 59, 59, 59, 59, 59, 41, 35, 41, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 132, 59, 59, 59, 59, 59, 59, 35, 35, 1, 59, 59, 59] 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])
total number of confs: 522
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278078 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278078
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278078/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278078
Building REAL300025278079
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278079'
/scratch/stefan/7808390/working/building/REAL300025278079 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278079

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278079/0 /scratch/stefan/7808390/working/building/REAL300025278079 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/978
`/scratch/stefan/7808390/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC1=O)

`REAL300025278079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278079 none CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 4, 4, 6, 1, 1, 1, 6] 7
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278079 none CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 6, 6, 6, 1] 7
rigid atoms, others: [0, 1, 2, 3, 4, 32, 46, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278079 none CN1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 7] 7
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: 11
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278079 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278079
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278079/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278079
Building REAL300025278080
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278080'
/scratch/stefan/7808390/working/building/REAL300025278080 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278080

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278080/0 /scratch/stefan/7808390/working/building/REAL300025278080 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/979
`/scratch/stefan/7808390/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278080 none C=CC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 130, 201, 201, 130, 130, 57, 57, 57, 57, 57, 36, 30, 36, 11, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 57, 57, 57, 57, 57, 57, 30, 30, 1, 57, 57, 57] 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])
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: REAL300025278080 none C=CC(C)(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 57, 57, 57, 57, 57, 1, 1, 29, 29, 29, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 57, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278080 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278080
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278080/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278080
Building REAL300025278081
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278081'
/scratch/stefan/7808390/working/building/REAL300025278081 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278081

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278081/0 /scratch/stefan/7808390/working/building/REAL300025278081 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/980
`/scratch/stefan/7808390/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278081 none C#CCCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 184, 199, 184, 184, 55, 55, 55, 29, 29, 29, 29, 29, 20, 18, 20, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 199, 199, 199, 199, 199, 199, 184, 184, 55, 29, 29, 29, 29, 29, 29, 18, 18, 1, 29, 29, 29] 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])
total number of confs: 981
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278081 none C#CCCCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 51, 44, 36, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 29, 29, 29, 29, 29, 1, 1, 53, 53, 53, 51, 51, 51, 51, 51, 51, 36, 36, 5, 1, 1, 1, 1, 1, 1, 4, 4, 29, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 348
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278081 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278081
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278081/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278081
Building REAL300025278082
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278082'
/scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025278082

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278082/0 /scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/981
`/scratch/stefan/7808390/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278082 none C[N@@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 30, 78, 78, 78, 78, 78, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 1, 20, 20, 78, 1, 1, 1] 127
rigid atoms, others: [48, 43, 47, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 171
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278082 none C[N@@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 24, 24, 61, 77, 127, 127, 127, 127, 127, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 61, 61, 127, 7, 7, 7] 127
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 334
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: REAL300025278082 none C[N@@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 78, 78, 78, 78, 78, 55, 46, 55, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 78, 78, 78, 78, 78, 78, 46, 46, 1, 78, 78, 78] 127
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49])
total number of confs: 402
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `1'
/scratch/stefan/7808390/working/building/REAL300025278082/1 /scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 1 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/982
`/scratch/stefan/7808390/working/3D/982' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278082.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025278082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278082/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278082 none C[N@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 24, 102, 102, 102, 102, 102, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 16, 16, 102, 1, 1, 1] 201
rigid atoms, others: [48, 43, 47, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
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: REAL300025278082 none C[N@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 16, 16, 16, 16, 16, 29, 29, 80, 112, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 80, 80, 201, 16, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025278082 none C[N@H+]1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 189, 201, 189, 189, 102, 102, 102, 102, 102, 68, 48, 68, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 102, 102, 102, 102, 102, 102, 48, 48, 1, 102, 102, 102] 201
rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49])
total number of confs: 617
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390
mkdir: created directory `2'
/scratch/stefan/7808390/working/building/REAL300025278082/2 /scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 2 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/983
`/scratch/stefan/7808390/working/3D/983' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278082.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025278082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278082/2/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: REAL300025278082 none CN1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 25, 96, 96, 96, 96, 96, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 11, 11, 96, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278082 none CN1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 14, 14, 14, 14, 14, 26, 26, 63, 110, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 14, 14, 63, 63, 201, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025278082 none CN1CCC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 201, 196, 196, 96, 96, 96, 96, 96, 64, 46, 64, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 96, 96, 96, 96, 96, 96, 46, 46, 1, 96, 96, 96] 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])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278082 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278082
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
2: /scratch/stefan/7808390/working/building/REAL300025278082/2.*
1: /scratch/stefan/7808390/working/building/REAL300025278082/1.*
0: /scratch/stefan/7808390/working/building/REAL300025278082/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278082
Building REAL300025278083
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278083'
/scratch/stefan/7808390/working/building/REAL300025278083 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278083

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278083/0 /scratch/stefan/7808390/working/building/REAL300025278083 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/984
`/scratch/stefan/7808390/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278083 none C[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 22, 22, 22, 5, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 13, 60, 60, 60, 60, 60, 1, 1, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 8, 8, 60, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 145
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: REAL300025278083 none C[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 11, 11, 11, 22, 22, 22, 22, 22, 37, 37, 72, 106, 201, 201, 201, 201, 201, 22, 22, 2, 2, 2, 1, 1, 11, 22, 22, 22, 22, 22, 22, 72, 72, 201, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 528
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: REAL300025278083 none C[C@@H]1C[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 98, 201, 98, 98, 60, 60, 60, 60, 60, 41, 32, 41, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 98, 60, 60, 60, 60, 60, 60, 32, 32, 1, 60, 60, 60] 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])
total number of confs: 638
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278083 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278083
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278083/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278083
Building REAL300025278084
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278084'
/scratch/stefan/7808390/working/building/REAL300025278084 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278084

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278084/0 /scratch/stefan/7808390/working/building/REAL300025278084 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/985
`/scratch/stefan/7808390/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278084 none O=C(CC1CC=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 7, 33, 33, 33, 33, 33, 1, 1, 33, 33, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 1, 1, 1, 1, 1, 1, 4, 4, 33, 1, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 50, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278084 none O=C(CC1CC=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 46, 46, 46, 46, 46, 54, 54, 75, 112, 201, 201, 201, 201, 201, 46, 46, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 46, 46, 46, 46, 46, 46, 75, 75, 201, 46, 46, 46] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025278084 none O=C(CC1CC=CCC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 83, 200, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 25, 23, 25, 11, 1, 1, 1, 1, 1, 1, 1, 33, 33, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 33, 33, 33, 33, 33, 33, 23, 23, 1, 33, 33, 33] 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])
total number of confs: 748
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278084 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278084
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278084/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278084
Building REAL300025278085
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278085'
/scratch/stefan/7808390/working/building/REAL300025278085 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278085

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278085/0 /scratch/stefan/7808390/working/building/REAL300025278085 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/986
`/scratch/stefan/7808390/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1)

`REAL300025278085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278085 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 62, 62, 62, 62, 62, 1, 1, 19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 10, 10, 62, 1, 1, 1, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 41, 42, 43, 44, 45, 46])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278085 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 7, 7, 19, 19, 19, 19, 19, 29, 29, 67, 100, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 2, 2, 2, 7, 19, 19, 19, 19, 19, 19, 67, 67, 201, 19, 19, 19, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 22, 23, 24] set([3, 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, 38, 39, 40])
total number of confs: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278085 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 72, 72, 72, 62, 62, 62, 62, 62, 46, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 72, 62, 62, 62, 62, 62, 62, 30, 30, 1, 62, 62, 62, 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])
total number of confs: 585
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278085 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278085
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278085/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278085
Building REAL300025278086
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278086'
/scratch/stefan/7808390/working/building/REAL300025278086 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278086

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278086/0 /scratch/stefan/7808390/working/building/REAL300025278086 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/987
`/scratch/stefan/7808390/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C[C@@H]1C[C@H]1C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025278086 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 7, 5, 5, 7, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 6, 6, 6, 6, 1, 6, 1, 1, 1, 60, 60, 62, 62, 62, 62, 62, 81, 81, 96, 132, 201, 201, 201, 201, 201, 62, 62, 20, 20, 6, 6, 1, 1, 1, 1, 1, 60, 62, 62, 62, 62, 62, 62, 96, 96, 201, 62, 62, 62] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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.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: REAL300025278086 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 7, 5, 5, 7, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 160, 200, 200, 200, 200, 200, 201, 201, 51, 51, 51, 51, 51, 43, 29, 43, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 160, 160, 200, 200, 201, 201, 201, 201, 201, 57, 51, 51, 51, 51, 51, 51, 29, 29, 1, 51, 51, 51] 201
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50])
total number of confs: 763
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278086 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 7, 5, 5, 7, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 33, 33, 33, 33, 33, 48, 48, 62, 94, 200, 200, 200, 200, 200, 33, 33, 7, 7, 1, 1, 6, 6, 6, 6, 6, 32, 33, 33, 33, 33, 33, 33, 62, 62, 200, 33, 33, 33] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 458
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278086 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 7, 5, 5, 7, 5, 5, 5, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 11, 33, 33, 33, 33, 33, 62, 62, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 51, 51, 51, 51, 51, 1, 1, 11, 11, 33, 33, 62, 62, 62, 62, 62, 3, 1, 1, 1, 1, 1, 1, 6, 6, 51, 1, 1, 1] 201
rigid atoms, others: [48, 43, 49, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 50, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 268
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278086 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278086
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278086/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278086
Building REAL300025278087
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278087'
/scratch/stefan/7808390/working/building/REAL300025278087 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278087

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278087/0 /scratch/stefan/7808390/working/building/REAL300025278087 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/988
`/scratch/stefan/7808390/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025278087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278087 none CC1COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 42, 101, 101, 101, 101, 101, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 27, 28, 101, 1, 1, 1, 15, 15] 150
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 46, 47])
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: REAL300025278087 none CC1COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 30, 30, 77, 99, 150, 150, 150, 150, 150, 15, 15, 1, 2, 2, 2, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 77, 77, 150, 15, 15, 15, 1, 1] 150
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 47, 25, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 419
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278087 none CC1COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [150, 150, 150, 150, 138, 138, 138, 101, 101, 101, 101, 101, 69, 40, 69, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 150, 150, 150, 150, 150, 150, 150, 150, 138, 101, 101, 101, 101, 101, 101, 40, 40, 1, 101, 101, 101, 150, 150] 150
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: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278087 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278087
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278087/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278087
Building REAL300025278088
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278088'
/scratch/stefan/7808390/working/building/REAL300025278088 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278088

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278088/0 /scratch/stefan/7808390/working/building/REAL300025278088 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/989
`/scratch/stefan/7808390/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3CCC4)C2C1)

`REAL300025278088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278088 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3CCC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 12, 12, 62, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 138
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278088 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3CCC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 44, 62, 62, 62, 62, 62, 95, 95, 95, 201, 201, 201, 201, 201, 201, 62, 62, 33, 33, 1, 62, 62, 62, 62, 62, 62, 95, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62] 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: 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: REAL300025278088 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@]34C[C@H]3CCC4)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 33, 67, 104, 201, 201, 201, 201, 201, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 67, 67, 201, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47])
total number of confs: 489
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278088 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278088
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278088/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278088
Building REAL300025278089
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278089'
/scratch/stefan/7808390/working/building/REAL300025278089 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278089

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278089/0 /scratch/stefan/7808390/working/building/REAL300025278089 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/990
`/scratch/stefan/7808390/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1OCC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278089 none CC[C@@H]1OCC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 8, 8, 8, 3, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 4, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 3, 3, 7, 1, 1, 1] 11
rigid atoms, others: [48, 43, 49, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 50, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278089 none CC[C@@H]1OCC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 9, 11, 11, 11, 11, 11, 11, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 9, 9, 11, 8, 8, 8] 11
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 37] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025278089 none CC[C@@H]1OCC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7] 11
rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50])
total number of confs: 22
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278089 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278089
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278089/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278089
Building REAL300025278090
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278090'
/scratch/stefan/7808390/working/building/REAL300025278090 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278090

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278090/0 /scratch/stefan/7808390/working/building/REAL300025278090 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/991
`/scratch/stefan/7808390/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=N1)

`REAL300025278090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278090 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [29, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 14, 67, 67, 67, 67, 67, 1, 1, 13, 13, 13, 29, 29, 29, 29, 29, 3, 1, 1, 1, 1, 1, 1, 8, 8, 67, 1, 1, 1, 13, 13] 131
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46])
total number of confs: 197
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: REAL300025278090 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 13, 20, 20, 39, 59, 113, 113, 113, 113, 113, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 9, 13, 13, 13, 13, 13, 13, 39, 39, 113, 13, 13, 13, 1, 1] 131
rigid atoms, others: [1, 2, 3, 4, 45, 46, 24, 25, 26] set([0, 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])
total number of confs: 294
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: REAL300025278090 none CCC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)NC=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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [131, 113, 113, 80, 80, 80, 67, 67, 67, 67, 67, 51, 31, 51, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 113, 113, 113, 131, 131, 131, 131, 131, 80, 67, 67, 67, 67, 67, 67, 31, 31, 1, 67, 67, 67, 113, 113] 131
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])
total number of confs: 419
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278090 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278090
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278090/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278090
Building REAL300025278091
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278091'
/scratch/stefan/7808390/working/building/REAL300025278091 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278091

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278091/0 /scratch/stefan/7808390/working/building/REAL300025278091 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/992
`/scratch/stefan/7808390/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278091 none CC1=NNC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 22, 96, 96, 96, 96, 96, 1, 1, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 12, 12, 96, 1, 1, 1] 201
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278091 none CC1=NNC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 21, 21, 21, 21, 21, 31, 31, 67, 104, 201, 201, 201, 201, 201, 21, 21, 2, 2, 2, 1, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 67, 67, 201, 21, 21, 21] 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])
total number of confs: 498
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278091 none CC1=NNC(C)=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 154, 154, 154, 96, 96, 96, 96, 96, 64, 50, 64, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 201, 201, 154, 96, 96, 96, 96, 96, 96, 50, 50, 1, 96, 96, 96] 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])
total number of confs: 576
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278091 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278091
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278091/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278091
Building REAL300025278092
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278092'
/scratch/stefan/7808390/working/building/REAL300025278092 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278092

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278092/0 /scratch/stefan/7808390/working/building/REAL300025278092 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/993
`/scratch/stefan/7808390/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278092 none CC1=NC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 18, 52, 52, 52, 52, 52, 1, 1, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 14, 14, 52, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 45, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278092 none CC1=NC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 9, 9, 9, 33, 33, 33, 33, 33, 57, 57, 115, 147, 201, 201, 201, 201, 201, 33, 33, 2, 2, 2, 1, 1, 1, 9, 33, 33, 33, 33, 33, 33, 115, 115, 201, 33, 33, 33] 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: 612
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278092 none CC1=NC=CC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 115, 115, 115, 52, 52, 52, 52, 52, 35, 32, 35, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 115, 52, 52, 52, 52, 52, 52, 32, 32, 1, 52, 52, 52] 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])
total number of confs: 489
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278092 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278092
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278092/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278092
Building REAL300025278093
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278093'
/scratch/stefan/7808390/working/building/REAL300025278093 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278093

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278093/0 /scratch/stefan/7808390/working/building/REAL300025278093 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/994
`/scratch/stefan/7808390/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278093 none CC(C)CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 201, 167, 196, 67, 67, 67, 31, 31, 31, 31, 31, 24, 22, 24, 11, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 67, 31, 31, 31, 31, 31, 31, 22, 22, 1, 31, 31, 31] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 1219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278093 none CC(C)CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 52, 52, 42, 39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 31, 31, 31, 31, 31, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 39, 39, 6, 1, 1, 1, 1, 1, 1, 4, 4, 31, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 381
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278093 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278093
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278093/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278093
Building REAL300025278094
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278094'
/scratch/stefan/7808390/working/building/REAL300025278094 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278094

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278094/0 /scratch/stefan/7808390/working/building/REAL300025278094 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/995
`/scratch/stefan/7808390/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[NH+](CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278094 none CC[NH+](CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 129, 129, 129, 49, 49, 49, 49, 49, 30, 30, 30, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 49, 49, 49, 49, 49, 49, 30, 30, 1, 49, 49, 49] 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])
total number of confs: 737
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: REAL300025278094 none CC[NH+](CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 33, 46, 46, 46, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 49, 49, 49, 49, 49, 1, 1, 47, 47, 47, 47, 47, 46, 46, 46, 46, 46, 33, 33, 6, 1, 1, 1, 1, 1, 1, 6, 6, 49, 1, 1, 1] 201
rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 49, 50, 51, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 265
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278094 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278094
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278094/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278094
Building REAL300025278095
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278095'
/scratch/stefan/7808390/working/building/REAL300025278095 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278095

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278095/0 /scratch/stefan/7808390/working/building/REAL300025278095 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/996
`/scratch/stefan/7808390/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278095 none CCC(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 191, 201, 191, 191, 76, 76, 76, 76, 76, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 191, 76, 76, 76, 76, 76, 76, 39, 39, 1, 76, 76, 76] 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])
total number of confs: 622
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278095 none CCC(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 76, 76, 76, 76, 76, 1, 1, 29, 29, 29, 29, 29, 17, 6, 1, 1, 1, 1, 1, 1, 8, 8, 76, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278095 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278095
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278095/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278095
Building REAL300025278096
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278096'
/scratch/stefan/7808390/working/building/REAL300025278096 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278096

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278096/0 /scratch/stefan/7808390/working/building/REAL300025278096 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/997
`/scratch/stefan/7808390/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278096 none O=C(CCCF)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [95, 95, 95, 195, 201, 201, 41, 41, 41, 41, 41, 30, 26, 30, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 195, 195, 201, 201, 201, 201, 95, 41, 41, 41, 41, 41, 41, 26, 26, 1, 41, 41, 41] 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])
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: REAL300025278096 none O=C(CCCF)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 33, 43, 52, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 41, 41, 41, 41, 41, 1, 1, 33, 33, 50, 50, 49, 48, 6, 1, 1, 1, 1, 1, 1, 6, 6, 41, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278096 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278096
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278096/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278096
Building REAL300025278097
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278097'
/scratch/stefan/7808390/working/building/REAL300025278097 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278097

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278097/0 /scratch/stefan/7808390/working/building/REAL300025278097 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/998
`/scratch/stefan/7808390/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(F)(F)F)

`REAL300025278097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278097 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 118, 118, 118, 57, 57, 57, 57, 57, 38, 32, 38, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 118, 57, 57, 57, 57, 57, 57, 32, 32, 1, 57, 57, 57] 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])
total number of confs: 772
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278097 none CC(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 57, 57, 57, 57, 57, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 9, 9, 57, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278097 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278097
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278097/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278097
Building REAL300025278098
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278098'
/scratch/stefan/7808390/working/building/REAL300025278098 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278098

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278098/0 /scratch/stefan/7808390/working/building/REAL300025278098 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/999
`/scratch/stefan/7808390/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278098 none CC1=COC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 20, 20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 68, 68, 68, 68, 68, 1, 1, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 9, 9, 68, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 137
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278098 none CC1=COC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 9, 9, 9, 20, 20, 20, 20, 20, 34, 34, 65, 99, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 1, 1, 9, 20, 20, 20, 20, 20, 20, 65, 65, 201, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 511
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: REAL300025278098 none CC1=COC=C1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 12, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 127, 127, 127, 68, 68, 68, 68, 68, 48, 34, 48, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 127, 68, 68, 68, 68, 68, 68, 34, 34, 1, 68, 68, 68] 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])
total number of confs: 523
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278098 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278098
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278098/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278098
Building REAL300025278099
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278099'
/scratch/stefan/7808390/working/building/REAL300025278099 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278099

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278099/0 /scratch/stefan/7808390/working/building/REAL300025278099 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1000
`/scratch/stefan/7808390/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278099 none C[C@H]1C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [30, 30, 30, 30, 6, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 13, 63, 63, 63, 63, 63, 1, 1, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 8, 8, 63, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278099 none C[C@H]1C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 10, 10, 10, 30, 30, 30, 30, 30, 41, 41, 74, 115, 201, 201, 201, 201, 201, 30, 30, 2, 2, 2, 1, 1, 10, 30, 30, 30, 30, 30, 30, 74, 74, 201, 30, 30, 30] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 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: 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: REAL300025278099 none C[C@H]1C[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 114, 201, 114, 114, 63, 63, 63, 63, 63, 47, 41, 47, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 114, 63, 63, 63, 63, 63, 63, 41, 41, 1, 63, 63, 63] 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])
total number of confs: 654
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278099 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278099
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278099/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278099
Building REAL300025278100
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278100'
/scratch/stefan/7808390/working/building/REAL300025278100 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278100

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278100/0 /scratch/stefan/7808390/working/building/REAL300025278100 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1001
`/scratch/stefan/7808390/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CCC1)

`REAL300025278100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278100 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 16, 64, 64, 64, 64, 64, 1, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 10, 10, 64, 1, 1, 1, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21, 41, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43, 44, 45, 46, 47])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278100 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 35, 35, 67, 105, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 67, 67, 201, 19, 19, 19, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 22, 23, 24, 25] set([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: 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: REAL300025278100 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 99, 99, 99, 64, 64, 64, 64, 64, 48, 40, 48, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 99, 64, 64, 64, 64, 64, 64, 40, 40, 1, 64, 64, 64, 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])
total number of confs: 646
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278100 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278100
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278100/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278100
Building REAL300025278101
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278101'
/scratch/stefan/7808390/working/building/REAL300025278101 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278101

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278101/0 /scratch/stefan/7808390/working/building/REAL300025278101 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1002
`/scratch/stefan/7808390/working/3D/1002' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278101 none CN1C(=O)CC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 14, 14, 14, 6, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 101, 101, 101, 101, 101, 1, 1, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 14, 14, 101, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 47, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 194
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: REAL300025278101 none CN1C(=O)CC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 6, 6, 14, 14, 14, 14, 14, 25, 25, 64, 98, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 64, 64, 201, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 31] set([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, 46, 47])
total number of confs: 486
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: REAL300025278101 none CN1C(=O)CC[C@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 166, 201, 166, 166, 101, 101, 101, 101, 101, 73, 46, 73, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 166, 101, 101, 101, 101, 101, 101, 46, 46, 1, 101, 101, 101] 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])
total number of confs: 654
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278101 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278101
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278101/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278101
Building REAL300025278102
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278102'
/scratch/stefan/7808390/working/building/REAL300025278102 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278102

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278102/0 /scratch/stefan/7808390/working/building/REAL300025278102 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1003
`/scratch/stefan/7808390/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=N1)

`REAL300025278102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278102 none CN1N=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 38, 102, 102, 102, 102, 102, 1, 1, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 23, 23, 102, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 36, 37, 38])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278102 none CN1N=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 4, 4, 4, 17, 17, 17, 17, 17, 40, 40, 109, 150, 201, 201, 201, 201, 201, 17, 17, 1, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 109, 109, 201, 17, 17, 17] 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])
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: REAL300025278102 none CN1N=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 180, 180, 180, 102, 102, 102, 102, 102, 64, 41, 64, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 180, 102, 102, 102, 102, 102, 102, 41, 41, 1, 102, 102, 102] 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])
total number of confs: 597
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278102 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278102
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278102/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278102
Building REAL300025278103
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278103'
/scratch/stefan/7808390/working/building/REAL300025278103 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278103

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278103/0 /scratch/stefan/7808390/working/building/REAL300025278103 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1004
`/scratch/stefan/7808390/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278103 none CC1(C)CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 47, 146, 146, 146, 146, 146, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 1, 21, 21, 146, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 264
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278103 none CC1(C)CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 3, 7, 7, 7, 7, 7, 19, 19, 52, 96, 201, 201, 201, 201, 201, 7, 7, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 52, 52, 201, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 38, 39, 37] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 451
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278103 none CC1(C)CCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 146, 146, 146, 146, 146, 97, 50, 97, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 146, 146, 146, 146, 146, 146, 50, 50, 1, 146, 146, 146] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 588
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278103 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278103
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278103/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278103
Building REAL300025278104
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278104'
/scratch/stefan/7808390/working/building/REAL300025278104 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278104

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278104/0 /scratch/stefan/7808390/working/building/REAL300025278104 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1005
`/scratch/stefan/7808390/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025278104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278104 none CC1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 37, 37, 37, 37, 37, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 36, 36, 6, 1, 1, 1, 1, 1, 1, 5, 5, 37, 1, 1, 1, 52, 52] 201
rigid atoms, others: [43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 50, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 52])
total number of confs: 238
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278104 none CC1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 52, 52, 52, 52, 52, 65, 65, 86, 124, 201, 201, 201, 201, 201, 52, 52, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 20, 52, 52, 52, 52, 52, 52, 86, 86, 201, 52, 52, 52, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 35, 52, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
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: REAL300025278104 none CC1CCC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 78, 78, 78, 37, 37, 37, 37, 37, 26, 23, 26, 11, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 78, 37, 37, 37, 37, 37, 37, 23, 23, 1, 37, 37, 37, 201, 201] 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, 52])
total number of confs: 740
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278104 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278104
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278104/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278104
Building REAL300025278105
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278105'
/scratch/stefan/7808390/working/building/REAL300025278105 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278105

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278105/0 /scratch/stefan/7808390/working/building/REAL300025278105 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1006
`/scratch/stefan/7808390/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N(C)N=C1)

`REAL300025278105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278105 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 16, 62, 62, 62, 62, 62, 1, 1, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 9, 9, 62, 1, 1, 1, 21, 21, 21, 21] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46])
total number of confs: 134
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: REAL300025278105 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 21, 21, 21, 21, 21, 32, 32, 63, 94, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 63, 63, 201, 21, 21, 21, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 46, 23, 24, 25, 26] set([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, 42, 43, 44, 45])
total number of confs: 485
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: REAL300025278105 none CC1=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 99, 99, 99, 62, 62, 62, 62, 62, 46, 39, 46, 12, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 99, 62, 62, 62, 62, 62, 62, 39, 39, 1, 62, 62, 62, 201, 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: 492
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278105 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278105
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278105/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278105
Building REAL300025278106
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278106'
/scratch/stefan/7808390/working/building/REAL300025278106 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278106

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278106/0 /scratch/stefan/7808390/working/building/REAL300025278106 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1007
`/scratch/stefan/7808390/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278106 none CC(C)C(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 201, 167, 184, 167, 167, 66, 66, 66, 66, 66, 42, 32, 42, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 184, 167, 66, 66, 66, 66, 66, 66, 32, 32, 1, 66, 66, 66] 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])
total number of confs: 694
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278106 none CC(C)C(F)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 32, 6, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 66, 66, 66, 66, 66, 1, 1, 33, 33, 33, 33, 33, 33, 33, 16, 6, 1, 1, 1, 1, 1, 1, 7, 7, 66, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 24, 39, 45] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278106 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278106
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278106/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278106
Building REAL300025278107
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278107'
/scratch/stefan/7808390/working/building/REAL300025278107 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278107

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278107/0 /scratch/stefan/7808390/working/building/REAL300025278107 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1008
`/scratch/stefan/7808390/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1)

`REAL300025278107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278107 none CCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 22, 70, 70, 70, 70, 70, 1, 1, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 12, 12, 70, 1, 1, 1, 17, 17, 17, 17, 17, 17] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 46, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50, 51, 52])
total number of confs: 217
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278107 none CCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 27, 27, 60, 96, 199, 199, 199, 199, 199, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 6, 17, 17, 17, 17, 17, 17, 60, 60, 199, 17, 17, 17, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 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])
total number of confs: 479
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278107 none CCCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 122, 122, 122, 70, 70, 70, 70, 70, 48, 24, 48, 12, 1, 1, 1, 1, 1, 1, 1, 70, 70, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 122, 70, 70, 70, 70, 70, 70, 24, 24, 1, 70, 70, 70, 199, 199, 199, 199, 199, 199] 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, 52])
total number of confs: 674
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278107 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278107
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278107/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278107
Building REAL300025278108
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278108'
/scratch/stefan/7808390/working/building/REAL300025278108 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278108

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278108/0 /scratch/stefan/7808390/working/building/REAL300025278108 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1009
`/scratch/stefan/7808390/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278108 none C=CC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 201, 142, 142, 64, 64, 64, 64, 64, 44, 34, 44, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 64, 64, 64, 64, 64, 64, 34, 34, 1, 64, 64, 64] 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])
total number of confs: 779
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278108 none C=CC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 21, 22, 6, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 64, 64, 64, 64, 64, 1, 1, 27, 27, 27, 22, 22, 22, 22, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 7, 7, 64, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278108 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278108
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278108/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278108
Building REAL300025278109
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278109'
/scratch/stefan/7808390/working/building/REAL300025278109 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278109

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278109/0 /scratch/stefan/7808390/working/building/REAL300025278109 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1010
`/scratch/stefan/7808390/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1)

`REAL300025278109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278109 none CCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 22, 89, 89, 89, 89, 89, 1, 1, 15, 15, 15, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 13, 13, 89, 1, 1, 1, 15, 15, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 21, 22, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 46, 47, 48, 49])
total number of confs: 184
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278109 none CCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 6, 6, 6, 15, 15, 15, 15, 15, 28, 28, 56, 94, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 6, 15, 15, 15, 15, 15, 15, 56, 56, 201, 15, 15, 15, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 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])
total number of confs: 452
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278109 none CCC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 144, 144, 144, 89, 89, 89, 89, 89, 66, 41, 66, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 144, 89, 89, 89, 89, 89, 89, 41, 41, 1, 89, 89, 89, 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])
total number of confs: 656
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278109 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278109
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278109/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278109
Building REAL300025278110
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278110'
/scratch/stefan/7808390/working/building/REAL300025278110 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278110

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278110/0 /scratch/stefan/7808390/working/building/REAL300025278110 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1011
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)C3CC4(CCC4)C3)C2C1)

`REAL300025278110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278110 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4(CCC4)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 10, 18, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 1, 1, 10, 10, 45, 1, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1] 145
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 48, 49, 50, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 141
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: REAL300025278110 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4(CCC4)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [38, 31, 12, 1, 1, 1, 1, 1, 1, 1, 38, 45, 45, 45, 45, 45, 60, 60, 60, 145, 145, 145, 145, 145, 145, 45, 45, 31, 31, 1, 45, 45, 45, 45, 45, 45, 60, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 45, 45, 45] 145
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: 449
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: REAL300025278110 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CC4(CCC4)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [37, 22, 37, 66, 98, 145, 145, 145, 145, 145, 22, 22, 22, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 22, 22, 66, 66, 145, 22, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22] 145
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50])
total number of confs: 406
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278110 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278110
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278110/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278110
Building REAL300025278111
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278111'
/scratch/stefan/7808390/working/building/REAL300025278111 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278111

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278111/0 /scratch/stefan/7808390/working/building/REAL300025278111 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1012
`/scratch/stefan/7808390/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC#CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278111 none CC#CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 140, 155, 45, 45, 45, 22, 22, 22, 22, 22, 17, 16, 17, 9, 1, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 176, 175, 191, 191, 155, 155, 45, 22, 22, 22, 22, 22, 22, 16, 16, 1, 22, 22, 22] 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])
total number of confs: 1069
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278111 none CC#CCCCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 22, 22, 22, 22, 22, 1, 1, 59, 59, 59, 54, 55, 48, 48, 33, 33, 6, 1, 1, 1, 1, 1, 1, 4, 4, 22, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278111 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278111
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278111/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278111
Building REAL300025278112
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278112'
/scratch/stefan/7808390/working/building/REAL300025278112 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278112

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278112/0 /scratch/stefan/7808390/working/building/REAL300025278112 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1013
`/scratch/stefan/7808390/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3[C@@H]4COC[C@@H]43)C2C1)

`REAL300025278112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278112 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3[C@@H]4COC[C@@H]43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 10, 16, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 10, 10, 74, 1, 1, 1, 1, 1, 1, 5, 30, 30, 30, 30, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 44, 10, 11, 12, 13, 14, 15, 43, 45, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 38, 39, 40, 41, 42])
total number of confs: 180
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: REAL300025278112 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3[C@@H]4COC[C@@H]43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 74, 74, 74, 74, 74, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 74, 74, 34, 34, 1, 74, 74, 74, 74, 74, 74, 120, 201, 201, 201, 201, 74, 74, 74] 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: 642
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: REAL300025278112 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3[C@@H]4COC[C@@H]43)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 30, 45, 83, 119, 201, 201, 201, 201, 201, 30, 30, 30, 30, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 83, 83, 201, 30, 30, 30, 30, 30, 30, 12, 1, 1, 1, 1, 30, 30, 30] 201
rigid atoms, others: [39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 547
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278112 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278112
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278112/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278112
Building REAL300025278113
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278113'
/scratch/stefan/7808390/working/building/REAL300025278113 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278113

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278113/0 /scratch/stefan/7808390/working/building/REAL300025278113 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1014
`/scratch/stefan/7808390/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278113 none O=C(CCCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 31, 35, 56, 56, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 28, 28, 28, 28, 28, 1, 1, 27, 27, 35, 35, 35, 35, 56, 56, 56, 56, 56, 5, 1, 1, 1, 1, 1, 1, 4, 4, 28, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
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: REAL300025278113 none O=C(CCCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 7, 3, 3, 1, 1, 1, 1, 20, 20, 56, 56, 56, 56, 56, 66, 66, 88, 117, 201, 201, 201, 201, 201, 56, 56, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 20, 56, 56, 56, 56, 56, 56, 88, 88, 201, 56, 56, 56] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 36] 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, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025278113 none O=C(CCCC1CC1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 160, 160, 168, 201, 201, 28, 28, 28, 28, 28, 21, 19, 21, 9, 1, 1, 1, 1, 1, 1, 1, 28, 28, 160, 160, 168, 168, 168, 168, 201, 201, 201, 201, 201, 60, 28, 28, 28, 28, 28, 28, 19, 19, 1, 28, 28, 28] 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])
total number of confs: 837
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278113 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278113
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278113/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278113
Building REAL300025278114
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278114'
/scratch/stefan/7808390/working/building/REAL300025278114 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278114

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278114/0 /scratch/stefan/7808390/working/building/REAL300025278114 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1015
`/scratch/stefan/7808390/working/3D/1015' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1=O)

`REAL300025278114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278114 none CN1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 21, 80, 80, 80, 80, 80, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 15, 15, 80, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 24, 39, 47, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278114 none CN1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 8, 8, 8, 30, 30, 30, 30, 30, 59, 59, 121, 151, 201, 201, 201, 201, 201, 30, 30, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 30, 121, 121, 201, 30, 30, 30] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 612
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278114 none CN1CCC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 168, 168, 168, 80, 80, 80, 80, 80, 51, 39, 51, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 80, 80, 80, 80, 80, 80, 39, 39, 1, 80, 80, 80] 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])
total number of confs: 617
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278114 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278114
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278114/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278114
Building REAL300025278115
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278115'
/scratch/stefan/7808390/working/building/REAL300025278115 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278115

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278115/0 /scratch/stefan/7808390/working/building/REAL300025278115 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1016
`/scratch/stefan/7808390/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(OCC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278115 none CCCC(OCC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 126, 157, 157, 157, 126, 126, 49, 49, 49, 49, 49, 30, 26, 30, 11, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 157, 126, 49, 49, 49, 49, 49, 49, 26, 26, 1, 49, 49, 49] 201
rigid atoms, others: [49, 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, 50, 51, 52])
total number of confs: 791
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278115 none CCCC(OCC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 11, 6, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 49, 49, 49, 49, 49, 1, 1, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 6, 6, 49, 1, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 52, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278115 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278115
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278115/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278115
Building REAL300025278116
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278116'
/scratch/stefan/7808390/working/building/REAL300025278116 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278116

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278116/0 /scratch/stefan/7808390/working/building/REAL300025278116 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1017
`/scratch/stefan/7808390/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278116 none CC1(C)CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 25, 103, 103, 103, 103, 103, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 13, 13, 103, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 193
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: REAL300025278116 none CC1(C)CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 14, 14, 14, 14, 14, 25, 25, 63, 103, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 63, 63, 201, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 493
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: REAL300025278116 none CC1(C)CCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 181, 181, 103, 103, 103, 103, 103, 74, 42, 74, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 103, 103, 103, 103, 103, 103, 42, 42, 1, 103, 103, 103] 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])
total number of confs: 639
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278116 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278116
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278116/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278116
Building REAL300025278117
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278117'
/scratch/stefan/7808390/working/building/REAL300025278117 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278117

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278117/0 /scratch/stefan/7808390/working/building/REAL300025278117 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1018
`/scratch/stefan/7808390/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C1)

`REAL300025278117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278117 none CC1=COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 41, 117, 117, 117, 117, 117, 1, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 25, 25, 117, 1, 1, 1, 11] 172
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43])
total number of confs: 242
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: REAL300025278117 none CC1=COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 31, 31, 84, 113, 172, 172, 172, 172, 172, 11, 11, 1, 2, 2, 2, 1, 5, 11, 11, 11, 11, 11, 11, 84, 84, 172, 11, 11, 11, 1] 172
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: 477
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: REAL300025278117 none CC1=COC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [172, 172, 172, 172, 167, 167, 167, 117, 117, 117, 117, 117, 72, 42, 72, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 172, 172, 172, 172, 172, 167, 117, 117, 117, 117, 117, 117, 42, 42, 1, 117, 117, 117, 172] 172
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: 515
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278117 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278117
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278117/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278117
Building REAL300025278118
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278118'
/scratch/stefan/7808390/working/building/REAL300025278118 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278118

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278118/0 /scratch/stefan/7808390/working/building/REAL300025278118 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1019
`/scratch/stefan/7808390/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC(=O)N3)C2C1)

`REAL300025278118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278118 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [2, 1, 2, 9, 14, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 5, 5, 5, 28, 28, 28, 28, 28, 1, 1, 9, 9, 55, 1, 1, 1, 1, 1, 1, 5, 28, 28, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 40, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278118 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [39, 35, 13, 1, 1, 1, 1, 1, 1, 1, 39, 55, 55, 55, 55, 55, 115, 115, 115, 201, 201, 201, 201, 201, 55, 55, 35, 35, 1, 55, 55, 55, 55, 55, 55, 115, 201, 201, 55, 55, 55] 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])
total number of confs: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278118 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CSC(=O)N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [38, 28, 38, 86, 126, 201, 201, 201, 201, 201, 28, 28, 28, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 86, 86, 201, 28, 28, 28, 28, 28, 28, 10, 1, 1, 28, 28, 28] 201
rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 549
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278118 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278118
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278118/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278118
Building REAL300025278119
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278119'
/scratch/stefan/7808390/working/building/REAL300025278119 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278119

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278119/0 /scratch/stefan/7808390/working/building/REAL300025278119 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1020
`/scratch/stefan/7808390/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278119 none C=CC(CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 167, 201, 201, 105, 105, 105, 48, 48, 48, 48, 48, 37, 32, 37, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 105, 48, 48, 48, 48, 48, 48, 32, 32, 1, 48, 48, 48] 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])
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: REAL300025278119 none C=CC(CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 29, 39, 39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 48, 48, 48, 48, 48, 1, 1, 40, 40, 40, 39, 39, 39, 39, 39, 39, 29, 29, 6, 1, 1, 1, 1, 1, 1, 5, 5, 48, 1, 1, 1] 201
rigid atoms, others: [43, 49, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46])
total number of confs: 229
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278119 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278119
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278119/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278119
Building REAL300025278120
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278120'
/scratch/stefan/7808390/working/building/REAL300025278120 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278120

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278120/0 /scratch/stefan/7808390/working/building/REAL300025278120 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1021
`/scratch/stefan/7808390/working/3D/1021' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1)

`REAL300025278120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278120 none CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [174, 103, 174, 103, 103, 53, 53, 53, 53, 53, 39, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 174, 201, 201, 174, 174, 174, 174, 174, 174, 103, 53, 53, 53, 53, 53, 53, 33, 33, 1, 53, 53, 53, 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])
total number of confs: 787
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: REAL300025278120 none CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 53, 53, 53, 53, 53, 1, 1, 15, 34, 34, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1, 1, 34, 34, 34, 34, 34] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 44, 43, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 45, 46, 47, 48, 49])
total number of confs: 196
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: REAL300025278120 none CC(C)(C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 10, 34, 34, 34, 34, 34, 43, 43, 70, 108, 201, 201, 201, 201, 201, 34, 34, 1, 1, 1, 7, 7, 7, 6, 6, 6, 10, 34, 34, 34, 34, 34, 34, 70, 70, 201, 34, 34, 34, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 45, 46, 47, 48, 49, 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, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 518
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278120 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278120
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278120/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278120
Building REAL300025278121
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278121'
/scratch/stefan/7808390/working/building/REAL300025278121 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278121

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278121/0 /scratch/stefan/7808390/working/building/REAL300025278121 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1022
`/scratch/stefan/7808390/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)N1CC2CC(NC(=O)[C@H]3C[C@H]4C[C@H]4C3)C2C1)

`REAL300025278121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278121 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3C[C@H]4C[C@H]4C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 15, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 8, 8, 62, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 21, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 47, 10, 11, 12, 13, 14, 15, 46, 45, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 147
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278121 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3C[C@H]4C[C@H]4C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 47, 62, 62, 62, 62, 62, 102, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 30, 30, 1, 62, 62, 62, 62, 62, 62, 102, 201, 201, 201, 201, 201, 201, 62, 62, 62] 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: 642
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: REAL300025278121 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)[C@H]3C[C@H]4C[C@H]4C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 21, 31, 64, 99, 201, 201, 201, 201, 201, 21, 21, 21, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 64, 64, 201, 21, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21] 201
rigid atoms, others: [39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47])
total number of confs: 489
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278121 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278121
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278121/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278121
Building REAL300025278122
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278122'
/scratch/stefan/7808390/working/building/REAL300025278122 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278122

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278122/0 /scratch/stefan/7808390/working/building/REAL300025278122 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1023
`/scratch/stefan/7808390/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CON=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278122 none O=C(CC1=CON=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 11, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 50, 50, 50, 50, 50, 1, 1, 11, 11, 26, 26, 4, 1, 1, 1, 1, 1, 1, 6, 6, 50, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278122 none O=C(CC1=CON=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 13, 13, 26, 26, 26, 26, 26, 40, 40, 61, 92, 201, 201, 201, 201, 201, 26, 26, 5, 5, 1, 1, 13, 26, 26, 26, 26, 26, 26, 61, 61, 201, 26, 26, 26] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29] set([0, 1, 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: 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: REAL300025278122 none O=C(CC1=CON=C1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 1, 12, 8, 1, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [83, 83, 83, 124, 201, 201, 201, 201, 50, 50, 50, 50, 50, 36, 24, 36, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 124, 124, 201, 201, 83, 50, 50, 50, 50, 50, 50, 24, 24, 1, 50, 50, 50] 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])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278122 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278122
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278122/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278122
Building REAL300025278123
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278123'
/scratch/stefan/7808390/working/building/REAL300025278123 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278123

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278123/0 /scratch/stefan/7808390/working/building/REAL300025278123 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1024
`/scratch/stefan/7808390/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278123 none CN1C(=O)CC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 14, 14, 14, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 32, 118, 118, 118, 118, 118, 1, 1, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 17, 17, 118, 1, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 47, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 222
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278123 none CN1C(=O)CC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 6, 6, 6, 14, 14, 14, 14, 14, 29, 29, 70, 110, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 70, 70, 201, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 31] set([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, 46, 47])
total number of confs: 488
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: REAL300025278123 none CN1C(=O)CC[C@@H]1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', '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, 7, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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, 173, 201, 173, 173, 118, 118, 118, 118, 118, 81, 45, 81, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 173, 118, 118, 118, 118, 118, 118, 45, 45, 1, 118, 118, 118] 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])
total number of confs: 635
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278123 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278123
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278123/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278123
Building REAL300025278124
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278124'
/scratch/stefan/7808390/working/building/REAL300025278124 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278124

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278124/0 /scratch/stefan/7808390/working/building/REAL300025278124 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1025
`/scratch/stefan/7808390/working/3D/1025' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)C1)

`REAL300025278124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278124 none CC1(C)CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 33, 33, 33, 33, 33, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 5, 1, 1, 1, 1, 1, 1, 4, 4, 33, 1, 1, 1, 46, 46] 201
rigid atoms, others: [43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 50, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 52])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278124 none CC1(C)CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 16, 16, 16, 46, 46, 46, 46, 46, 56, 56, 78, 115, 201, 201, 201, 201, 201, 46, 46, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 4, 16, 46, 46, 46, 46, 46, 46, 78, 78, 201, 46, 46, 46, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 51, 33, 34, 35, 52, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278124 none CC1(C)CC(CC(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 134, 75, 75, 75, 33, 33, 33, 33, 33, 23, 21, 23, 9, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 134, 75, 33, 33, 33, 33, 33, 33, 21, 21, 1, 33, 33, 33, 201, 201] 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, 52])
total number of confs: 817
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278124 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278124
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278124/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278124
Building REAL300025278125
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278125'
/scratch/stefan/7808390/working/building/REAL300025278125 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278125

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278125/0 /scratch/stefan/7808390/working/building/REAL300025278125 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1026
`/scratch/stefan/7808390/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOC3)C2C1)

`REAL300025278125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278125 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens 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, 10, 17, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 1, 1, 10, 10, 72, 1, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 18, 18, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 42, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 157
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278125 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 72, 72, 72, 72, 72, 130, 130, 130, 201, 201, 201, 201, 201, 72, 72, 35, 35, 1, 72, 72, 72, 72, 72, 72, 130, 201, 201, 201, 201, 201, 201, 72, 72, 72] 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])
total number of confs: 677
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: REAL300025278125 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3(F)CCOC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 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]
0  hydrogens 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, 30, 66, 106, 201, 201, 201, 201, 201, 18, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 66, 66, 201, 18, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 35, 42, 43, 44])
total number of confs: 519
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278125 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278125
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278125/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278125
Building REAL300025278126
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278126'
/scratch/stefan/7808390/working/building/REAL300025278126 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278126

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278126/0 /scratch/stefan/7808390/working/building/REAL300025278126 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1027
`/scratch/stefan/7808390/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)N1C)

`REAL300025278126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278126 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 30, 78, 78, 78, 78, 78, 1, 1, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 17, 17, 78, 1, 1, 1, 21, 21, 21] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45, 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: REAL300025278126 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 21, 21, 21, 21, 21, 45, 45, 110, 140, 201, 201, 201, 201, 201, 21, 21, 1, 1, 2, 2, 2, 1, 6, 21, 21, 21, 21, 21, 21, 110, 110, 201, 21, 21, 21, 2, 2, 2] 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, 46])
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: REAL300025278126 none CC1=NC=C(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 144, 144, 144, 78, 78, 78, 78, 78, 52, 37, 52, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201, 201, 201, 201, 201, 201, 144, 78, 78, 78, 78, 78, 78, 37, 37, 1, 78, 78, 78, 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])
total number of confs: 561
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278126 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278126
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278126/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278126
Building REAL300025278127
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278127'
/scratch/stefan/7808390/working/building/REAL300025278127 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278127

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278127/0 /scratch/stefan/7808390/working/building/REAL300025278127 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1028
`/scratch/stefan/7808390/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278127 none CC(C)(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 107, 107, 107, 44, 44, 44, 44, 44, 29, 23, 29, 11, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 44, 44, 44, 44, 44, 44, 23, 23, 1, 44, 44, 44] 201
rigid atoms, others: [48, 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, 49, 50, 51])
total number of confs: 758
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278127 none CC(C)(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 38, 38, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 1, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278127 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278127
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278127/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278127
Building REAL300025278128
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278128'
/scratch/stefan/7808390/working/building/REAL300025278128 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278128

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278128/0 /scratch/stefan/7808390/working/building/REAL300025278128 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1029
`/scratch/stefan/7808390/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=N3)C2C1)

`REAL300025278128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278128 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 44, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 22, 22, 135, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 256
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278128 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 82, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 43, 43, 1, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 135, 135, 135] 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: 578
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278128 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=NC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 103, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 61, 61, 201, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 9, 9, 9] 201
rigid atoms, others: [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, 34, 35, 39, 40, 41])
total number of confs: 454
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278128 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278128
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278128/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278128
Building REAL300025278129
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278129'
/scratch/stefan/7808390/working/building/REAL300025278129 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278129

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278129/0 /scratch/stefan/7808390/working/building/REAL300025278129 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1030
`/scratch/stefan/7808390/working/3D/1030' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC=N1)

`REAL300025278129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278129 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC=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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 46, 46, 46, 46, 46, 1, 1, 20, 20, 6, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 8, 8, 46, 1, 1, 1, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 44, 45])
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: REAL300025278129 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC=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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 5, 5, 5, 20, 20, 20, 20, 20, 32, 32, 67, 113, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 2, 2, 2, 1, 5, 20, 20, 20, 20, 20, 20, 67, 67, 201, 20, 20, 20, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 24, 25, 26, 30] set([5, 6, 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])
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: REAL300025278129 none CC1=CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=CC=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', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 68, 68, 68, 46, 46, 46, 46, 46, 31, 27, 31, 12, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 68, 201, 201, 201, 201, 68, 46, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 46, 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])
total number of confs: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278129 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278129
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278129/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278129
Building REAL300025278130
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278130'
/scratch/stefan/7808390/working/building/REAL300025278130 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278130

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278130/0 /scratch/stefan/7808390/working/building/REAL300025278130 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1031
`/scratch/stefan/7808390/working/3D/1031' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278130 none O=C(CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 57, 57, 57, 57, 57, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 5, 5, 57, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 189
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278130 none O=C(CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 32, 32, 45, 45, 65, 111, 201, 201, 201, 201, 201, 32, 32, 3, 3, 1, 1, 1, 10, 32, 32, 32, 32, 32, 32, 65, 65, 201, 32, 32, 32] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025278130 none O=C(CC1=CC=CO1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 1, 12, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [138, 138, 138, 201, 201, 201, 201, 201, 57, 57, 57, 57, 57, 37, 30, 37, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 138, 57, 57, 57, 57, 57, 57, 30, 30, 1, 57, 57, 57] 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])
total number of confs: 784
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278130 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278130
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278130/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278130
Building REAL300025278131
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278131'
/scratch/stefan/7808390/working/building/REAL300025278131 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278131

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278131/0 /scratch/stefan/7808390/working/building/REAL300025278131 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1032
`/scratch/stefan/7808390/working/3D/1032' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=N3)C2C1)

`REAL300025278131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278131 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 40, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 6, 11, 11, 1, 1, 21, 21, 129, 1, 1, 1, 1, 1, 1, 6, 11, 6, 11, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278131 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens 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, 55, 13, 1, 1, 1, 1, 1, 1, 1, 89, 129, 129, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 55, 55, 1, 129, 129, 129, 129, 129, 129, 201, 201, 201, 201, 129, 129, 129] 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: 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: REAL300025278131 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens 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, 30, 78, 116, 201, 201, 201, 201, 201, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 18, 18, 78, 78, 201, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 18, 18, 18] 201
rigid atoms, others: [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, 34, 35, 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/7808390/working/building/REAL300025278131 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278131
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278131/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278131
Building REAL300025278132
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278132'
/scratch/stefan/7808390/working/building/REAL300025278132 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278132

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278132/0 /scratch/stefan/7808390/working/building/REAL300025278132 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1033
`/scratch/stefan/7808390/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278132 none CCC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 120, 63, 63, 63, 30, 30, 30, 30, 30, 24, 21, 24, 11, 1, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 120, 120, 63, 30, 30, 30, 30, 30, 30, 21, 21, 1, 30, 30, 30] 201
rigid atoms, others: [48, 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, 49, 50, 51])
total number of confs: 948
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278132 none CCC(C)CCC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 56, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 30, 30, 30, 30, 30, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 32, 32, 30, 30, 5, 1, 1, 1, 1, 1, 1, 4, 4, 30, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278132 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278132
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278132/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278132
Building REAL300025278133
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278133'
/scratch/stefan/7808390/working/building/REAL300025278133 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278133

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278133/0 /scratch/stefan/7808390/working/building/REAL300025278133 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1034
`/scratch/stefan/7808390/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=N3)C2C1)

`REAL300025278133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278133 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 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, 7, 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]
0  hydrogens 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, 18, 34, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 18, 18, 122, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 39, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38])
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: REAL300025278133 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 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, 7, 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]
0  hydrogens 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, 50, 13, 1, 1, 1, 1, 1, 1, 1, 79, 122, 122, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 50, 50, 1, 122, 122, 122, 122, 122, 122, 201, 201, 201, 201, 122, 122, 122] 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: 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: REAL300025278133 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CC=CN=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 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, 7, 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]
0  hydrogens 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, 12, 24, 73, 120, 201, 201, 201, 201, 201, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 73, 73, 201, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 12, 12, 12] 201
rigid atoms, others: [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, 34, 35, 39, 40, 41])
total number of confs: 486
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278133 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278133
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278133/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278133
Building REAL300025278134
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278134'
/scratch/stefan/7808390/working/building/REAL300025278134 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278134

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278134/0 /scratch/stefan/7808390/working/building/REAL300025278134 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1035
`/scratch/stefan/7808390/working/3D/1035' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1)

`REAL300025278134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278134 none CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 48, 117, 117, 117, 117, 117, 1, 1, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 27, 27, 117, 1, 1, 1, 12, 12, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45])
total number of confs: 252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278134 none CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 4, 4, 4, 12, 12, 12, 12, 12, 33, 33, 104, 148, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 2, 2, 2, 4, 12, 12, 12, 12, 12, 12, 104, 104, 201, 12, 12, 12, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 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])
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: REAL300025278134 none CC1=NC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 200, 200, 200, 117, 117, 117, 117, 117, 72, 42, 72, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 200, 117, 117, 117, 117, 117, 117, 42, 42, 1, 117, 117, 117, 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, 44, 45])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278134 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278134
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278134/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278134
Building REAL300025278135
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278135'
/scratch/stefan/7808390/working/building/REAL300025278135 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278135

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278135/0 /scratch/stefan/7808390/working/building/REAL300025278135 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1036
`/scratch/stefan/7808390/working/3D/1036' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278135 none O=C(CCN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 8, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 6, 26, 30, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 27, 27, 27, 27, 27, 1, 1, 26, 26, 30, 30, 46, 6, 1, 1, 1, 1, 1, 1, 5, 5, 27, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 44, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 39, 40, 41])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278135 none O=C(CCN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 8, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 20, 20, 46, 46, 46, 46, 46, 56, 56, 77, 122, 201, 201, 201, 201, 201, 46, 46, 9, 9, 5, 5, 1, 20, 46, 46, 46, 46, 46, 46, 77, 77, 201, 46, 46, 46] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025278135 none O=C(CCN1C=NN=N1)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 8, 8, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [85, 85, 85, 194, 195, 201, 201, 201, 201, 27, 27, 27, 27, 27, 19, 17, 19, 10, 1, 1, 1, 1, 1, 1, 1, 27, 27, 194, 194, 195, 195, 201, 85, 27, 27, 27, 27, 27, 27, 17, 17, 1, 27, 27, 27] 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278135 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278135
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278135/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278135
Building REAL300025278136
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278136'
/scratch/stefan/7808390/working/building/REAL300025278136 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278136

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278136/0 /scratch/stefan/7808390/working/building/REAL300025278136 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1037
`/scratch/stefan/7808390/working/3D/1037' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=C3F)C2C1)

`REAL300025278136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278136 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 14, 27, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1, 14, 14, 99, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278136 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 61, 99, 99, 99, 99, 99, 200, 200, 200, 201, 201, 201, 201, 201, 201, 99, 99, 43, 43, 1, 99, 99, 99, 99, 99, 99, 200, 201, 201, 201, 99, 99, 99] 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: 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: REAL300025278136 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=NC=CC=C3F)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 5, 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, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 14, 25, 64, 106, 201, 201, 201, 201, 201, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 64, 64, 201, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 14, 14, 14] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 471
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278136 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278136
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278136/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278136
Building REAL300025278137
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278137'
/scratch/stefan/7808390/working/building/REAL300025278137 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278137

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278137/0 /scratch/stefan/7808390/working/building/REAL300025278137 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1038
`/scratch/stefan/7808390/working/3D/1038' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278137 none CC1OCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 26, 79, 79, 79, 79, 79, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 14, 14, 79, 1, 1, 1] 90
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44])
total number of confs: 154
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278137 none CC1OCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 10, 10, 25, 42, 90, 90, 90, 90, 90, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 25, 25, 90, 6, 6, 6] 90
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 202
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: REAL300025278137 none CC1OCCC1C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 79, 79, 79, 79, 79, 55, 34, 55, 12, 1, 1, 1, 1, 1, 1, 1, 79, 79, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 79, 79, 79, 79, 79, 79, 34, 34, 1, 79, 79, 79] 90
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])
total number of confs: 265
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278137 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278137
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278137/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278137
Building REAL300025278138
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278138'
/scratch/stefan/7808390/working/building/REAL300025278138 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278138

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278138/0 /scratch/stefan/7808390/working/building/REAL300025278138 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1039
`/scratch/stefan/7808390/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOC1)

`REAL300025278138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278138 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 39, 125, 125, 125, 125, 125, 1, 1, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 19, 19, 125, 1, 1, 1, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21, 41, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 42, 43, 44, 45, 46, 47])
total number of confs: 238
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: REAL300025278138 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  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, 4, 11, 11, 11, 11, 11, 26, 26, 59, 104, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 11, 59, 59, 201, 11, 11, 11, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 22, 23, 24, 25] set([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: 463
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: REAL300025278138 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need 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, 125, 125, 125, 125, 125, 82, 47, 82, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201, 177, 125, 125, 125, 125, 125, 125, 47, 47, 1, 125, 125, 125, 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])
total number of confs: 604
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278138 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278138
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278138/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278138
Building REAL300025278139
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278139'
/scratch/stefan/7808390/working/building/REAL300025278139 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278139

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278139/0 /scratch/stefan/7808390/working/building/REAL300025278139 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1040
`/scratch/stefan/7808390/working/3D/1040' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278139 none CCC(CC)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 201, 174, 174, 111, 111, 111, 111, 111, 71, 45, 71, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 111, 111, 111, 111, 111, 111, 45, 45, 1, 111, 111, 111] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278139 none CCC(CC)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 111, 111, 111, 111, 111, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 10, 10, 111, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278139 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278139
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278139/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278139
Building REAL300025278140
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278140'
/scratch/stefan/7808390/working/building/REAL300025278140 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278140

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278140/0 /scratch/stefan/7808390/working/building/REAL300025278140 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1041
`/scratch/stefan/7808390/working/3D/1041' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCO1)

`REAL300025278140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278140 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCO1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [32, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 18, 55, 55, 55, 55, 55, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 14, 14, 55, 1, 1, 1, 32, 32, 32, 32] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 46, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 47, 48, 49, 50])
total number of confs: 180
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278140 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCO1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 11, 11, 11, 32, 32, 32, 32, 32, 52, 52, 108, 141, 201, 201, 201, 201, 201, 32, 32, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 11, 32, 32, 32, 32, 32, 32, 108, 108, 201, 32, 32, 32, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 48, 49, 50, 24, 25, 26, 30, 31] set([5, 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: 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: REAL300025278140 none CC1CC(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCO1 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.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 115, 115, 115, 55, 55, 55, 55, 55, 34, 31, 34, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 55, 55, 55, 55, 55, 55, 31, 31, 1, 55, 55, 55, 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])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278140 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278140
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278140/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278140
Building REAL300025278141
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278141'
/scratch/stefan/7808390/working/building/REAL300025278141 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278141

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278141/0 /scratch/stefan/7808390/working/building/REAL300025278141 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1042)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1042
`/scratch/stefan/7808390/working/3D/1042' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278141 none CCCC(C)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 124, 186, 186, 187, 124, 124, 43, 43, 43, 43, 43, 28, 21, 28, 11, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 187, 187, 187, 187, 187, 124, 43, 43, 43, 43, 43, 43, 21, 21, 1, 43, 43, 43] 201
rigid atoms, others: [51, 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, 50, 52, 53, 54])
total number of confs: 786
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278141 none CCCC(C)(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 6, 15, 15, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 43, 43, 43, 43, 43, 1, 1, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 5, 5, 43, 1, 1, 1] 201
rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 52, 14, 54, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 49, 50, 51])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278141 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278141
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278141/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278141
Building REAL300025278142
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278142'
/scratch/stefan/7808390/working/building/REAL300025278142 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278142

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278142/0 /scratch/stefan/7808390/working/building/REAL300025278142 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1043)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1043
`/scratch/stefan/7808390/working/3D/1043' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278142 none CCC(CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 85, 85, 85, 49, 49, 49, 49, 49, 37, 32, 37, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 49, 49, 49, 49, 49, 49, 32, 32, 1, 49, 49, 49] 201
rigid atoms, others: [48, 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, 49, 50, 51])
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: REAL300025278142 none CCC(CC)CC(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 49, 49, 49, 49, 49, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 49, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278142 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278142
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278142/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278142
Building REAL300025278143
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278143'
/scratch/stefan/7808390/working/building/REAL300025278143 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278143

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278143/0 /scratch/stefan/7808390/working/building/REAL300025278143 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1044)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1044
`/scratch/stefan/7808390/working/3D/1044' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278143 none CCC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 127, 201, 127, 127, 67, 67, 67, 67, 67, 42, 30, 42, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 67, 67, 67, 67, 67, 67, 30, 30, 1, 67, 67, 67] 201
rigid atoms, others: [48, 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, 49, 50, 51])
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: REAL300025278143 none CCC(C)C(C)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 21, 6, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 67, 67, 67, 67, 67, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 5, 5, 67, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 172
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278143 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278143
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278143/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278143
Building REAL300025278144
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278144'
/scratch/stefan/7808390/working/building/REAL300025278144 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278144

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278144/0 /scratch/stefan/7808390/working/building/REAL300025278144 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1045)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1045
`/scratch/stefan/7808390/working/3D/1045' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21)

`REAL300025278144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278144 none CCCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 172, 104, 172, 172, 104, 104, 42, 42, 42, 42, 42, 30, 27, 30, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 172, 172, 172, 104, 42, 42, 42, 42, 42, 42, 27, 27, 1, 42, 42, 42] 201
rigid atoms, others: [48, 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, 49, 50, 51])
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: REAL300025278144 none CCCC(CC)C(=O)NC1CC2CN(C(=O)CSC3=NNC(=O)[N-]3)CC21 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 42, 42, 42, 42, 42, 1, 1, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 42, 1, 1, 1] 201
rigid atoms, others: [45, 43, 49, 8, 9, 10, 11, 12, 13, 14, 44, 40, 50, 51, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278144 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278144
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278144/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278144
Building REAL300025278145
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278145'
/scratch/stefan/7808390/working/building/REAL300025278145 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278145

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278145/0 /scratch/stefan/7808390/working/building/REAL300025278145 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1046)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1046
`/scratch/stefan/7808390/working/3D/1046' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(=O)NCC3CC3)C2C1)

`REAL300025278145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278145 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(=O)NCC3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need 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, 5, 9, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 38, 38, 1, 1, 5, 5, 61, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 38, 38, 38, 38, 38, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 46, 45, 25, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 214
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278145 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(=O)NCC3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 13, 1, 1, 1, 1, 1, 1, 1, 34, 61, 61, 61, 61, 61, 152, 152, 152, 152, 152, 152, 199, 201, 201, 61, 61, 28, 28, 1, 61, 61, 61, 61, 61, 61, 152, 152, 199, 199, 201, 201, 201, 201, 201, 61, 61, 61] 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: 701
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278145 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C(=O)NCC3CC3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 53, 80, 124, 201, 201, 201, 201, 201, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 38, 38, 80, 80, 201, 38, 38, 38, 38, 38, 38, 15, 15, 5, 5, 1, 1, 1, 1, 1, 38, 38, 38] 201
rigid atoms, others: [40, 41, 42, 43, 44, 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, 45, 46, 47])
total number of confs: 561
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278145 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278145
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278145/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278145
Building REAL300025278146
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278146'
/scratch/stefan/7808390/working/building/REAL300025278146 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278146

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278146/0 /scratch/stefan/7808390/working/building/REAL300025278146 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1047)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1047
`/scratch/stefan/7808390/working/3D/1047' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCOC1)

`REAL300025278146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278146 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 27, 100, 100, 100, 100, 100, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 14, 14, 100, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 41, 36, 42, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 187
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: REAL300025278146 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 21, 21, 58, 98, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 11, 58, 58, 201, 11, 11, 11, 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: 475
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: REAL300025278146 none CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CCCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [201, 155, 155, 155, 100, 100, 100, 100, 100, 75, 52, 75, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 155, 100, 100, 100, 100, 100, 100, 52, 52, 1, 100, 100, 100, 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])
total number of confs: 639
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278146 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278146
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278146/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278146
Building REAL300025278147
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278147'
/scratch/stefan/7808390/working/building/REAL300025278147 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278147

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278147/0 /scratch/stefan/7808390/working/building/REAL300025278147 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1048)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1048
`/scratch/stefan/7808390/working/3D/1048' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(F)C3)C2C1)

`REAL300025278147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278147 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 9, 15, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 1, 9, 9, 56, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 44, 10, 11, 12, 13, 14, 15, 46, 45, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025278147 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 35, 13, 1, 1, 1, 1, 1, 1, 1, 41, 56, 56, 56, 56, 56, 117, 117, 117, 201, 201, 201, 201, 201, 56, 56, 35, 35, 1, 56, 56, 56, 56, 56, 56, 117, 201, 201, 201, 201, 201, 201, 201, 201, 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, 46])
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: REAL300025278147 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3CCC(F)C3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 26, 36, 76, 111, 201, 201, 201, 201, 201, 26, 26, 26, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 76, 76, 201, 26, 26, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 201
rigid atoms, others: [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, 35, 44, 45, 46])
total number of confs: 522
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278147 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278147
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278147/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278147
Building REAL300025278148
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278148'
/scratch/stefan/7808390/working/building/REAL300025278148 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278148

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278148/0 /scratch/stefan/7808390/working/building/REAL300025278148 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1049)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1049
`/scratch/stefan/7808390/working/3D/1049' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)CC1)

`REAL300025278148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278148 none C[NH+](C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 9, 1, 1, 1, 2, 2, 2, 2] 9
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 49, 50, 51, 52])
total number of confs: 28
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278148 none C[NH+](C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 9, 9, 9, 9, 9, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 2, 2, 2, 1, 1, 1, 1] 9
rigid atoms, others: [4, 5, 6, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 30
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: REAL300025278148 none C[NH+](C)CC1(C(=O)NC2CC3CN(C(=O)CSC4=NNC(=O)[N-]4)CC32)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', 'C.3', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9, 9, 9, 9] 9
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, 52])
total number of confs: 15
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278148 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278148
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278148/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278148
Building REAL300025278149
mkdir: created directory `/scratch/stefan/7808390/working/building/REAL300025278149'
/scratch/stefan/7808390/working/building/REAL300025278149 /scratch/stefan/7808390/working /scratch/stefan/7808390
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025278149

mkdir: created directory `0'
/scratch/stefan/7808390/working/building/REAL300025278149/0 /scratch/stefan/7808390/working/building/REAL300025278149 /scratch/stefan/7808390/working /scratch/stefan/7808390
Protomer 0 (index: 1050)
Found valid previously generated 3D confromation in /scratch/stefan/7808390/working/3D/1050
`/scratch/stefan/7808390/working/3D/1050' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNC(=O)C=N3)C2C1)

`REAL300025278149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025278149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7808390/working/building/REAL300025278149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025278149 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNC(=O)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [6, 1, 6, 18, 33, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 18, 18, 121, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 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: REAL300025278149 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNC(=O)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [76, 48, 13, 1, 1, 1, 1, 1, 1, 1, 76, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 48, 48, 1, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 121, 121, 121] 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: 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: REAL300025278149 none O=C(CSC1=NNC(=O)[N-]1)N1CC2CC(NC(=O)C3=CNC(=O)C=N3)C2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [23, 11, 23, 69, 116, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 69, 69, 201, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 11, 11, 11] 201
rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 472
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7808390/working/building/REAL300025278149 /scratch/stefan/7808390/working /scratch/stefan/7808390

Finished preparing REAL300025278149
Recording results
/scratch/stefan/7808390/working /scratch/stefan/7808390
Appending to /scratch/stefan/7808390/finished/xaaabka.*
0: /scratch/stefan/7808390/working/building/REAL300025278149/0.*
Removing working files in /scratch/stefan/7808390/working/building/REAL300025278149
/scratch/stefan/7808390
Compressing combined databse files
/scratch/stefan/7808390/finished/xaaabka.db2.gz
/scratch/stefan/7808390/finished/xaaabka.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7808390/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7808390/working/3D/1051'
removed directory: `/scratch/stefan/7808390/working/3D'
`/scratch/stefan/7808390/working/protonate' -> `/scratch/stefan/7808390/archive'
`/scratch/stefan/7808390/working/input-smiles.ism' -> `/scratch/stefan/7808390/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7808390/working/building'
rmdir: removing directory, `/scratch/stefan/7808390/working'
ls: No match.
ls: No match.